diff --git a/AdditionalFile1.xlsx b/AdditionalFile1.xlsx new file mode 100644 index 0000000..59914e2 Binary files /dev/null and b/AdditionalFile1.xlsx differ diff --git a/SNVs/SNVs_M129V.R b/SNVs/SNVs_M129V.R new file mode 100644 index 0000000..7a6c63c --- /dev/null +++ b/SNVs/SNVs_M129V.R @@ -0,0 +1,252 @@ +# Reviewer's question (paraphrased): +# M129V individuals tend to have a higher number of non-coding SNVs (Table 1). +# Are these SNVs occuring on the same haplotype? + +# packages ---------------------------------------------------------------- + +library(openxlsx) +library(here) +library(dplyr) +library(tidyr) +library(tibble) +library(data.table) + + +# which samples are M129V ------------------------------------------------- +# look in samples sheet of AdditionalFile1 +meta <- read.xlsx('AdditionalFile1.xlsx', sheet='samples') + +mvs <- meta[which(meta$codon129=='M129V'), 'sample'] # mvs for M129V samples + + +# import phased VCFs for these samples ------------------------------------ + +# temporary list to store the VCFs +vcfs <- vector(mode='list', length=length(mvs)) + +# for each M129V sample +# build the path to its phased VCF file +# import it (i.e. add it to the list) +for (sp in 1:length(mvs)) { + # read.table() below understands it has to skip the header lines starting with # + # import that one vcf + vc <- read.table(here('haplotypephasing', 'vcf_phased', paste0(mvs[sp], '_whap.vcf')), sep='\t') + + # add the column names back + colnames(vc) <- c('chr', 'pos', 'id', 'ref', 'alt', 'qual', 'filter', 'info', 'format', 'phasing') + + # add the sample ID as first column + vc <- vc %>% + add_column(sampleid=mvs[sp], .before='chr') + + # add that vcf to the list + vcfs[[sp]] <- vc +} + +# now collapse the list in one dataframe +# below will overwrite the list, we do not need it anymore +vcfs <- as.data.frame(rbindlist(vcfs)) + + +# check that only one phase set in each VCF ------------------------------- + +# from https://whatshap.readthedocs.io/en/latest/guide.html +# under Phasing represented by PS (“phase set”) tag +# >> it can be that not all SNVs in the VCF are phased together +# below, we will assume that 1 or 0 refers to the same haplotype throughout each VCF, so we need to check this assumption + +# create new column phase set +vcfs$phaseset <- unlist(lapply(strsplit(vcfs$phasing, split=':'), function(s) {s[2]})) + +# simplify phasing column by removing phasingset info +vcfs$phasing <- unlist(lapply(strsplit(vcfs$phasing, split=':'), function(s) {s[1]})) + +# check all sample only have 1 phaseset +# below, counts number of distinct phasesets for each sample +vcfs %>% + group_by(sampleid) %>% + summarise(n_distinct(phaseset)) +# all 1, so OK to assume all SNVs for each sample are phased together + + +# get phasing info so M129V is always on the same haplotype --------------- +# within each sample, 1 or 0 is arbitrary +# below will be simpler is M129V is always on the same haplotype + +# is M129V always on the same haplotype? +# M129V is position chr20:4699605 +vcfs[which(vcfs$pos=='4699605'), 'phasing'] +# no, 4/9 are 0|1 and 5/9 are 1|0 +# this is essentially what you would expect + +# within any sample where M129V is 0|1, flip all the phasing info + +# small function to flip phasing info +flipPhase <- function(phase) { + + # sapply below so it can be ran on a vector directly + phaseflip <- sapply(phase, function(pha) { + + if (pha!='0|1' & pha!='1|0') { + stop('\t \t \t \t >>> Error: phasing info is not 1|0 or 0|1 \n') + } + + else if (pha=='0|1') { + return('1|0') + } + + else if (pha=='1|0') { + return('0|1') + } + + }) + + # simplify it + phaseflip <- as.vector(phaseflip) + + # return it + return(phaseflip) + +} +### + + +# which are the samples we need to flip? +# i.e. which are the rows where pos is 4699605 and phasing is 0|1 +flipsps <- vcfs[which(vcfs$pos=='4699605' & vcfs$phasing=='0|1') , 'sampleid'] # flip these samples + +# now to flip these samples +# take all the SNVs belonging to these samples and flip them +vcfs[which(vcfs$sampleid %in% flipsps), 'phasing'] <- flipPhase( vcfs[which(vcfs$sampleid %in% flipsps), 'phasing'] ) +# Note: do not need to do sample by sample +# for each sample, we need to flip all the phasing info once +# so same to flip all the SNVs at once + +### + +# now check that M129V always 1|0 +vcfs[which(vcfs$pos=='4699605'), 'phasing'] +# yes -- now all 1|0 + + +# for each SNVs, how many times is it phased with M129V? ------------------ + +# go through each unique SNV (by position), +# then for each sample which has this SNV, +# is it on the same haplotype as M129V? +# we set M129V to always be 1|0, so just need to count how many times it is 1|0 + +# first, for each SNV, count how many samples have it +wom <- vcfs %>% + group_by(pos) %>% + tally(name='n_samples') +# which will preallocate wom for with/without M129V + +# count by position by phase +n_pha <- vcfs %>% + group_by(pos, phasing) %>% + tally() + +# only the SNVs which were phased as 1|0: +n10 <- subset(n_pha, phasing=='1|0') +n10$phasing <- NULL # delete phasing info, we know it is 1|0 +# merge these samples count to wom +wom <- left_join(x=wom, y=n10, by='pos') + +# now repeat for SNVs which were phased as 0|1 +n01 <- subset(n_pha, phasing=='0|1') +n01$phasing <- NULL # delete phasing info, we know it is 0|1 +# merge these samples count to wom +wom <- left_join(x=wom, y=n01, by='pos') + +# now rename the column +colnames(wom) <- c('pos', 'n_samples', 'n_withM129V', 'n_woM129V') + +# everything that is still NA is actually 0 sample +wom$n_withM129V[is.na(wom$n_withM129V)] <- 0 +wom$n_woM129V[is.na(wom$n_woM129V)] <- 0 + +# few checks +# for each SNV, sum of number of samples which have it as 1|0 (i.e. with M129V) + number of samples which do not have it as 0|1 (i.e. without M129V) +# should be equal total number of samples with that SNV +unique(wom$n_withM129V + wom$n_woM129V == wom$n_samples) +# OK +# looking at the table: SNVs are always on one haplotype or the other + +# ! should delete M129V from the table otherwise we will be counting it +wom <- wom[-which(wom$pos==4699605),] + +# in summary +# out of 25 SNVs (not counting M129V), +nrow(subset(wom, n_withM129V>0 & n_woM129V==0)) +# 22 were always found with M129V + +nrow(subset(wom, n_woM129V>0 & n_withM129V==0)) +# only 3 SNVs were found not with M129V + +##### + +# in samples without M129V ------------------------------------------------ + +# you would expect to *never* find the 23 SNVs from above +# and only find the 3 SNVs (plus potentially others) + +#### + +# I think looking at phasing of the SNVs in the no-M129V samples is beyond the question +# will essentially consider them as all haplotypes not carrying M129V + +# as we will not use the phasing information, we can simply look at the AdditionalFile1 +# easier than deal with the VCFs + +# which samples do not carry M129V? --------------------------------------- +# look in samples sheet of AdditionalFile1 +meta <- read.xlsx('AdditionalFile1.xlsx', sheet='samples') + +ovs <- meta[which(meta$codon129!='M129V'), 'sample'] # ovs for other (not M129V) samples + +# import the SNVs +snvs <- read.xlsx('AdditionalFile1.xlsx', sheet='SNVs_filtered') + +# keep only the SNVs of the samples without M129V +snvo <- subset(snvs, SAMPLE %in% ovs) + + +# do any of the samples carry the 'with M129V-SNVs' ----------------------- + +# in the M129V samples, these SNVs are always found on the same haplotype +snv_with <- as.vector(unlist(wom[which(wom$n_withM129V > 0), 'pos'])) +# so you would expect to never find them in them in the no M129V samples + +intersect(snvo$POS, snv_with) +# 13 of 22 are found +# i.e. these 14 SNVs are NOT 'M129V specific' ** +# the other 9 seem M129V specific +# but difficult to be certain! It may be that we see them co-segregate in a larger cohort + +# the 9 that may be M129V specific are: +setdiff(snv_with, snvo$POS) + +subset(wom, pos %in% setdiff(snv_with, snvo$POS)) + +# ** for example, chr20:4690579 +# in M129V samples, it was only found on the M129V haplotype (9 of 9) +wom[which(wom$pos=='4690579'),] + +# however, it is also found in samples without M129V: +snvs[which(snvs$POS=='4690579' & snvs$SAMPLE %in% ovs),] # found in samples 46345, 52331, 55826 which is not M129V + +# !!! 52331 was not tested for M129V by Sanger, so written as not M129V +# but detected as M129V by Nanopore, so very likely M129V + + +# conversely... +# in the M129V samples, these SNVs are always found on the OTHER haplotype than M129V +snv_without <- as.vector(unlist(wom[which(wom$n_woM129V > 0), 'pos'])) +# so you would expect to find them in the no M129V samples + +intersect(snvo$POS, snv_without) +# 2 out of 3 are found +# not found: 4698921 but it was only present in one sample w/ M129V so relatively rare it seems +snvs[which(snvs$POS=='4698921'),] # of the whole cohort there is only sample with that SNV +# so roughly as expected: SNVs found on the other haplotype as M129V are also found in samples without M129V \ No newline at end of file diff --git a/SNVs/SNVscalls.R b/SNVs/SNVscalls.R new file mode 100644 index 0000000..9ad2f92 --- /dev/null +++ b/SNVs/SNVscalls.R @@ -0,0 +1,598 @@ +# work on SNVs called by nanopolish + + + +library(openxlsx) +library(here) +library(ggplot2) +library(dplyr) +library(tidyr) +library(stringr) +library(ggbeeswarm) + + + + +# colours ----------------------------------------------------------------- + +# cohorts + # inherited = yellow + # sCJD = khaki + # control = grey +cohcols <- c('#fcb505', '#78ac63', '#B3BDC4') + + + + +# import ------------------------------------------------------------------ + +# filtered SNVs +var <- read.xlsx(here('AdditionalFile1.xlsx'), sheet='SNVs_filtered') + +# unfiltered SNVs +varun <- read.xlsx(here('AdditionalFile1.xlsx'), sheet='SNVs_unfiltered') + +# samples metadata +meta <- read.xlsx(here('AdditionalFile1.xlsx'), sheet='samples') +meta$sample <- as.character(meta$sample) + +# SNV allele frequency +af <- read.xlsx(here('AdditionalFile1.xlsx'), sheet='SNVs_allelefrequency') + + + + +# how many total ---------------------------------------------------------- + +nrow(var) +# how many unique +length(unique(var$Existing_variation)) + + + + +# how many outside of protein-coding -------------------------------------- + +# column Consequence include missense_variant or else +# but careful; if SNV is at third base of codon, could be in coding region but not missense + +# all SNVs in coding region should have a number in column Protein_position +# (is not, it is '-', which will produce NA when converted to as.numeric, hence the Warning) +sum(is.na(as.numeric(var$Protein_position))) # number OUTSIDE coding region +sum(!is.na(as.numeric(var$Protein_position))) # number IN coding region + +# check we get the same when searching for the '-' +sum(var$Protein_position=='-') # number OUTSIDE coding region +sum(var$Protein_position!='-') # number IN coding region + +# check we are getting the same numbers using positions +# coding region = chr20:4,699,221--4,699,982 +length(which(var$POS < 4699221 | var$POS > 4699982)) # number OUTSIDE coding region +length(which(var$POS >= 4699221 & var$POS <= 4699982)) # number IN coding region +# same + +# add a tag to these SNVs for later +var$coding <- NA +var$coding[which(var$POS < 4699221 | var$POS > 4699982)] <- FALSE +var$coding[which(var$POS >= 4699221 & var$POS <= 4699982)] <- TRUE +# check no more NA +sum(is.na(var$coding)) + +# how many unique? + +# all +# create composite chr_pos_ref_alt column +var$com <- paste(var$CHROM, var$POS, var$REF, var$ALT, sep='_') +length(unique(var$com)) + +# coding +nrow(unique(subset(var, coding, com))) + +# non-coding +nrow(unique(subset(var, !coding, com))) + + + + +# how many in regulatory region ------------------------------------------- + +# regulatory region (according to Ensembl) = chr20:4,685,060–4,688,047 +subset(var, POS>4685060 & POS<4688047) +nrow(subset(var, POS>4685060 & POS<4688047)) +# how many unique? +nrow(unique(subset(var, POS>4685060 & POS<4688047, Existing_variation))) +# check same with com column +nrow(unique(subset(var, POS>4685060 & POS<4688047, com))) + +# how many affect transcription binding site in regulatory region +nrow(subset(var, POS>4685060 & POS<4688047 & Consequence=='TF_binding_site_variant')) +# how many unique? +nrow(unique(subset(var, POS>4685060 & POS<4688047 & Consequence=='TF_binding_site_variant', Existing_variation))) +# check same with com column +nrow(unique(subset(var, POS>4685060 & POS<4688047 & Consequence=='TF_binding_site_variant', com))) + + + +# how many non-coding per sample ------------------------------------------ + +nsnv_noncoding_persample <- var %>% + subset(!coding) %>% + group_by(SAMPLE) %>% + summarise(nsnsv=n()) + + + + +# versus Sanger ----------------------------------------------------------- + +# gather the Sanger SNV calls +snv129 <- meta[which(meta$codon129 == 'M129V'), c('individual', 'sample', 'codon129')] +colnames(snv129) <- c('invididual', 'sample', 'snv') +snv0 <- meta[which(meta$otherSNVs != '-'), c('individual', 'sample', 'otherSNVs')] +colnames(snv0) <- c('invididual', 'sample', 'snv') +san <- rbind(snv129, snv0) + +# add the nanopolish SNV calls in coding +nan <- subset(var, coding) %>% + select(SAMPLE, Protein_position, Amino_acids) +colnames(nan)[1] <- 'sample' +nan$sample <- as.character(nan$sample) + +# ! left_join, keep all Sanger calls +sana <- left_join(x=san, y=nan, by='sample') # Sanger vs Nanopolish +# ok + +# also do vice-versa so keep all nanopolish coding calls and add the Sanger +# (would pick up if anything extra from nanopolish, potentially false positive) +nasa <- left_join(x=nan, y=san, by='sample') # Nanopolish vs Sanger +# ok +# extra is PDG52331, codon129 was not tested by Sanger + + + + +# replicates when same invididual? ---------------------------------------- + +# i.e. matched blood vs brain samples + +# add all of meta information to var (will include individual) +var$SAMPLE <- as.character(var$SAMPLE) +varm <- left_join(var, meta, by=c('SAMPLE'='sample')) # var with metadata + +# check no individual is NA +varm[is.na(varm$individual),] + +# individuals in tissue comparison cohort +idvs <- as.numeric(unlist(unique(subset(meta, cohort=='inherited_tissuecomparison', individual)))) + +# will (semi) manually check the SNVs calls for each +# tally by composite ID; if all have 2, ok +subset(varm, individual==idvs[1]) %>% + group_by(com) %>% + tally() + +subset(varm, individual==idvs[2]) %>% + group_by(com) %>% + tally() + +subset(varm, individual==idvs[3]) %>% + group_by(com) %>% + tally() + +subset(varm, individual==idvs[4]) %>% + group_by(com) %>% + tally() + +# SNV below detected only in blood sample +varm[which(varm$com=='chr20_4690801_T_C'),] +# below, it is actually present, but only in unfiltered +# as it is above SOR threshold +subset(varun, SAMPLE==53689 & POS==4690801) + + + +# strand bias ------------------------------------------------------------- + +# from above, we know coding variants are all = Sanger +# (well, except PDG52331 which was not tested but will safe to assume it is M129V) + +# what is max strand bias of true positive calls = StrandOddsRatio threshold +max(subset(varm, coding, SOR)) + +# we set threshold at 1 +sorthr <- 1 + +# check we are obtaining same results +nrow(subset(varun, SOR% + group_by(com, rs, prion_disease) %>% + tally(name='nidvs') %>% + arrange(desc(nidvs)) # in order of most individuals to least + +# also need to group without prion_disease to get right descending order of SNVs +nin <- varmi %>% + group_by(com, rs) %>% + tally(name='nidvs') %>% + arrange(desc(nidvs)) # in order of most individuals to least + +# set the SNVs order as when grouped without looking at cohort (so most individuals >> least) +nindiv$rs <- factor(nindiv$rs, levels=nin$rs) + +# cohort in right order +nindiv$prion_disease <- factor(nindiv$prion_disease, levels=c('inherited', 'sCJD', 'control')) + +# y axis title +ytit <- paste0('number of individuals (of ', length(unique(meta$individual)), ')') # makes sure I do not do a mistake in the total number! + +SNVvsnInd <- ggplot(nindiv, aes(x=rs, y=nidvs, fill=prion_disease)) + + geom_col(position='stack', width=0.7) + + scale_fill_manual(values=cohcols) + + theme_minimal() + + theme( + legend.position='none', + axis.title.x=element_blank(), + panel.grid.minor.y=element_blank(), + axis.text.x=element_text(size=7, angle=90, hjust=0, vjust=0.40, margin=margin(t=0, r=0, b=0, l=0)), + axis.title.y=element_text(size=9, margin = margin(t=0, r=2, b=0, l=0)), + axis.text.y=element_text(size=7, margin = margin(t=0, r=0, b=0, l=0)), + ) + + ylab(ytit) + + scale_y_continuous(breaks=0:10) +SNVvsnInd +ggsave(here('SNVs', 'SNVvsnIndividuals.pdf'), plot=SNVvsnInd, width=120, height=80, units='mm') + + + + +# number of SNVs in each individual --------------------------------------- + +# group by individual and count +# during grouping, keep all info that is individual-level +nsnvi <- varmi %>% + group_by(individual, cohort, gDNA_tissue, prion_disease, + SV, codon129, otherSNVs, gender) %>% + tally(name='nsnvs') + +# ! any individual in meta but not in nsnvi, means it had 0 SNV, should add them +unique(meta$individual[!meta$individual %in% nsnvi$individual]) + +toadd <- meta[!meta$individual %in% nsnvi$individual , ] +# skip any brain samples +toadd <- subset(toadd, gDNA_tissue=='blood') + +# select the same column as above and add nsnvs = 0 +toadd <- toadd %>% + select(individual, cohort, gDNA_tissue, prion_disease, + SV, codon129, otherSNVs, gender) %>% + mutate(nsnvs=0) + +# add to nsnvi +nsnvi <- rbind(nsnvi, toadd) + + +# now there should be same number of rows as number of individuals +length(unique(meta$individual)) == nrow(nsnvi) + +# order individuals by number of SNVs +nsnvi <- nsnvi %>% + arrange(desc(nsnvs)) + +nsnvi$individual <- factor(nsnvi$individual, levels=nsnvi$individual) + +# now histogram SNV vs number of individuals who carry it +# (also colour by cohort) + +# temporarily increase a little bit the individuals with count 0 so we see the colour +nsnvi2 <- nsnvi +nsnvi2[which(nsnvi2$nsnvs==0), 'nsnvs'] <- nsnvi2[which(nsnvi2$nsnvs==0) , 'nsnvs'] + 0.1 + +# order of cohort +nsnvi2$prion_disease <- factor(nsnvi2$prion_disease, levels=c('inherited', 'sCJD', 'control')) + +individualvsnSNVs <- ggplot(nsnvi2, aes(x=individual, y=nsnvs, fill=prion_disease)) + + geom_col(width=0.8) + + scale_fill_manual(values=cohcols) + + theme_minimal() + + xlab('individual') + ylab('number of SNVs') + + theme( + panel.grid.minor.y=element_blank(), + legend.position='none') +individualvsnSNVs +ggsave(here('SNVs', 'individualvsnSNVs.pdf'), plot=individualvsnSNVs, width=200, height=100, units='mm') + + + + +# any cohort with more SNVs? ---------------------------------------------- + +# use nsnvi abvove + +nsnvi$prion_disease <- factor(nsnvi$prion_disease, levels=c('inherited', 'sCJD', 'control')) + +# plot +nsnvbyCoh <- ggplot(nsnvi, aes(x=prion_disease, y=nsnvs, colour=prion_disease)) + + geom_quasirandom(width=0.2, size=2) + + scale_colour_manual(values=cohcols) + + theme_minimal() + + theme( + legend.position='none', + panel.grid.minor.y=element_blank(), + axis.title.x=element_blank(), + axis.title.y=element_text(size=9, margin = margin(t=0, r=0, b=0, l=0)), + axis.text.x=element_text(angle=90, size=7, margin=margin(t=0, r=0, b=0, l=0), vjust=0.5), + axis.text.y=element_text(size=7, margin = margin(t=0, r=0, b=0, l=0)), + ) + + ylab('number of SNVs') + + scale_x_discrete(labels=c('inherited', 'sporadic', 'control')) +nsnvbyCoh + +ggsave(here('SNVs', 'SNVcountbyIndividualbyCohort.pdf'), plot=nsnvbyCoh, width=35, height=80, units='mm') + +# test +summary(aov(nsnvs ~ prion_disease, data=nsnvi)) + + + + +# same but only SNVs in regulatory region amplicon ------------------------ + +# i.e. before reverse primer of amplicon1 +varmireg <- subset(varmi, POS<4688028) + +# group by individual and count +# during grouping, keep all info that is individual-level +nsnvireg <- varmireg %>% + group_by(individual, cohort, gDNA_tissue, prion_disease, + SV, codon129, otherSNVs, gender) %>% + tally(name='nsnvs') + +# ! any individual in meta but not in nsnvireg, means it had 0 SNV in promoter, should add them +unique(meta$individual[!meta$individual %in% nsnvireg$individual]) + +toadd <- meta[!meta$individual %in% nsnvireg$individual , ] +# skip any brain samples +toadd <- subset(toadd, gDNA_tissue=='blood') + +# select the same column as above and add nsnvs = 0 +toadd <- toadd %>% + select(individual, cohort, gDNA_tissue, prion_disease, + SV, codon129, otherSNVs, gender) %>% + mutate(nsnvs=0) + +# add to nsnvi +nsnvireg <- rbind(nsnvireg, toadd) + +# now there should be same number of rows as number of individuals +length(unique(meta$individual)) == nrow(nsnvireg) + +# order individuals by number of SNVs +nsnvireg <- nsnvireg %>% + arrange(desc(nsnvs)) + +nsnvireg$individual <- factor(nsnvireg$individual, levels=nsnvireg$individual) + +# now histogram SNV vs number of individuals who carry it +# (also colour by cohort) + +# temporarily increase a little bit the individuals with count 0 so we see the colour +nsnvireg2 <- nsnvireg +nsnvireg2[which(nsnvireg2$nsnvs==0), 'nsnvs'] <- nsnvireg2[which(nsnvireg2$nsnvs==0) , 'nsnvs'] + 0.1 + +# order of cohorot +nsnvireg2$prion_disease <- factor(nsnvireg2$prion_disease, levels=c('inherited', 'sCJD', 'control')) + +individualvsnSNVsReg <- ggplot(nsnvireg2, aes(x=individual, y=nsnvs, fill=prion_disease)) + + geom_col(width=0.8) + + scale_fill_manual(values=cohcols) + + theme_minimal() + + xlab('individual') + ylab('number of SNVs') + + theme( + panel.grid.minor.y=element_blank(), + legend.position='none') +individualvsnSNVsReg +ggsave(here('SNVs', 'individualvsnSNVsReg.pdf'), plot=individualvsnSNVsReg, width=200, height=100, units='mm') + + +# any cohort with more SNVs in regulatory region? +# use nsnvireg above +nsnvireg$prion_disease <- factor(nsnvireg$prion_disease, levels=c('inherited', 'sCJD', 'control')) + +# plot +nsnvbyCohReg <- ggplot(nsnvireg, aes(x=prion_disease, y=nsnvs, colour=prion_disease)) + + geom_quasirandom(width=0.2, size=2) + + scale_colour_manual(values=cohcols) + + theme_minimal() + + theme( + legend.position='none', + panel.grid.minor.y=element_blank(), + axis.title.x=element_blank(), + axis.title.y=element_text(size=9, margin = margin(t=0, r=0, b=0, l=0)), + axis.text.x=element_text(size=7, margin=margin(t=0, r=0, b=0, l=0)), + axis.text.y=element_text(size=7, margin = margin(t=0, r=0, b=0, l=0)), + ) + + ylab('number of SNVs') + + scale_x_discrete(labels=c('inherited', 'sporadic', 'control')) +nsnvbyCohReg + +ggsave(here('SNVs', 'SNVcountbyIndividualbyCohortReg.pdf'), plot=nsnvbyCohReg, width=200, height=100, units='mm') + +# test +summary(aov(nsnvs ~ prion_disease, data=nsnvireg)) + + + + +# plot strand bias -------------------------------------------------------- + +# look at distribution +ggplot(varun, aes(SOR)) + + geom_histogram(binwidth=0.1) + +# add unique composite ID column +varun$ucom <- paste(varun$SAMPLE, varun$CHROM, varun$POS, varun$REF, varun$ALT, sep='_') +sum(duplicated(varun$uid)) # no duplicated + +# add coding or not in unfiltered SNVs +varun$coding <- NA +varun$coding[which(varun$POS < 4699221 | varun$POS > 4699982)] <- FALSE +varun$coding[which(varun$POS >= 4699221 & varun$POS <= 4699982)] <- TRUE + +varun <- varun[(order(varun$SOR)),] # order by SOR +varun$ucom <- factor(varun$ucom, levels=varun$ucom) + +# fix rs numbers as above +# some have multiple codes, just keep the rs +# it is the first one before the coma +varun$rs <- as.character(lapply(strsplit(varun$Existing_variation, ','), function(ex) {ex[1]})) + +# add a TRUE/FALSE column whether variation exists (has a RS number or not) +varun$variantHasRS <- sapply(varun$rs, function(v){ + if (v=='-') return(FALSE) + else return(TRUE) + }) + +# see below explanations for arrange() +# Update: after re-analysis, all have an rs number +# leaving code here, but it is not relevant anymore +var_SOR <- ggplot(varun %>% + arrange(desc(variantHasRS)), aes(x=ucom, y=SOR, colour=variantHasRS)) + + geom_hline(yintercept=sorthr, linetype=2, size=1.0, colour='#b8b8b8') + + geom_point(size=0.7) + + scale_colour_manual(values=c('#4D4D4D', '#f1876b')) + + theme_minimal() + + theme( + axis.text.x=element_blank(), + panel.grid.major.x=element_blank(), + panel.grid.minor.x=element_blank(), + axis.ticks.x=element_line(size=0.1), + legend.position='none', + axis.title.x=element_text(size=9, margin = margin(t=4, r=0, b=0, l=0)), + axis.title.y=element_text(size=9, margin = margin(t=0, r=2, b=0, l=0)), + axis.text.y=element_text(size=7, margin = margin(t=0, r=0, b=0, l=0)), + ) + + xlab('SNV call') + ylab('strand bias (SOR)') + + scale_x_discrete(expand=c(0.01,0)) +var_SOR +ggsave(here('SNVs', 'SOR.pdf'), plot=var_SOR, width=90, height=60, units='mm') + + +# same, but colour whether coding variant (so confirmed by Sanger, so true positive) or not +# add column 'confirmed by Sanger' or not +# basically, this is = coding SNVs from var + +varun$truepos <- FALSE + +# here are the SNVs we have in var +vfil <- unique(varm$ucom) # SNVs filtered + +# SNV is coding + SNV is in var = true positives +varun[which(varun$ucom %in% vfil & varun$coding) , 'truepos'] <- TRUE + +# ! need to plot the Sanger SNVs on top, otherwise will be hidden +# one way to do this is to put the coloured dots at the bottom of the dataframe, so gets drawn last +# this is what the arrange() below does +var_truepos <- ggplot(varun %>% + arrange(truepos), aes(x=ucom, y=SOR, colour=truepos)) + + geom_hline(yintercept=sorthr, linetype=2, size=1.0, colour='#b8b8b8') + + geom_point(size=0.7) + + scale_colour_manual(values=c('#4D4D4D', '#f1876b')) + + theme_minimal() + + theme( + axis.text.x=element_blank(), + panel.grid.major.x=element_blank(), + panel.grid.minor.x=element_blank(), + axis.ticks.x=element_line(size=0.1), + legend.position='none', + axis.title.x=element_text(size=9, margin = margin(t=4, r=0, b=0, l=0)), + axis.title.y=element_text(size=9, margin = margin(t=0, r=2, b=0, l=0)), + axis.text.y=element_text(size=7, margin = margin(t=0, r=0, b=0, l=0)) + ) + + xlab('SNV call') + ylab('strand bias (SOR)') + + scale_x_discrete(expand=c(0.01,0)) +var_truepos +ggsave(here('SNVs', 'SOR_truepositive.pdf'), plot=var_truepos, width=73, height=60, units='mm') + + + + +# number of individuals vs allele frequency ------------------------------- + +# use nin created above +# i.e. number of individuals who carry each unique SNV + +# join allele frequency to nin built above +colnames(af)[1] <- 'rs' +nin <- left_join(af, nin, by='rs') + +# check unique SNV +sum(duplicated(nin$rs)) + +# y axis title +ytit <- paste0('number of individuals (of ', length(unique(meta$individual)), ')') # makes sure I do not do a mistake in the total number! + +nvsaf <- ggplot(nin, aes(x=allelefrequency, y=nidvs)) + + geom_point(size=1.0) + + theme_minimal() + + scale_y_continuous(breaks=0:10) + + theme( + panel.grid.minor.y=element_blank(), + axis.title.x=element_text(size=9, margin = margin(t=2, r=0, b=0, l=0)), + axis.title.y=element_text(size=9, margin = margin(t=0, r=0, b=0, l=0)), + axis.text.x=element_text(size=7, margin=margin(t=0, r=0, b=0, l=0)), + axis.text.y=element_text(size=7, margin = margin(t=0, r=0, b=0, l=0)), + ) + + ylab(ytit) + xlab('allele frequency') +nvsaf + +ggsave(filename=here('SNVs', 'SNVcountindividualsvsAF.pdf'), plot=nvsaf, width=73, height=60, units='mm') + +cor(nin$nidvs, nin$allelefrequency, method='pearson') +cor.test(nin$nidvs, nin$allelefrequency, method='pearson') + +# there is one vaguely interesting SNV + +# low allele frequency but 8 individuals in our panel +intrs <- as.character(unlist(subset(nin, allelefrequency<0.15 & nidvs==8, rs))) # interesting rs +# who has it? +subset(varm, rs==intrs) + + + +# Ns ---------------------------------------------------------------------- + +# number of individuals in each cohort +nsnvi %>% + group_by(prion_disease) %>% + tally() diff --git a/SVs_sniffles/parseVCF.R b/SVs_sniffles/parseVCF.R new file mode 100644 index 0000000..052a8b7 --- /dev/null +++ b/SVs_sniffles/parseVCF.R @@ -0,0 +1,273 @@ +library(here) +library(data.table) +library(openxlsx) +library(dplyr) +library(tidyr) + + + + +# small functions --------------------------------------------------------- + +# function to pool columns from a dataframe into one column + # ! assumes that each row, there is only one element from the columns to pool which is not NA + # eg. at row 5, the columns we want to pool are NA, 9, NA >> gives 9 + # but if 2, 9, NA >> Error! (as more than one element) + + # usage example; poolColumns(df, c('col2', 'col5')) +poolColumns <- function(dataframe, vectorOfColNames) { + apply(dataframe, 1, function(row) { + tmp <- as.vector(unlist(c(row[vectorOfColNames]))) # concatenate the columns we need to pool at this row + # check there is only one not NA + if (sum(!is.na(tmp)) != 1) stop ('\t \t \t \t >>> Error: One or more rows has more than one element in the columns to be pooled \n') + # if ok, remove the NA and we are left with a single element + return(tmp[!is.na(tmp)]) # return for within the apply + }) +} + + + + +# import metadata --------------------------------------------------------- + +# import metadata +meta <- read.xlsx(here('supplementary.xlsx'), sheet='samples') + +# format meta + # - >> NA +meta$SV[which(meta$SV=='-')] <- NA + +# special case: PDG 46345 is 5 OPRI/1 OPRD + # make a new column SV2 for it (just for the 1 OPRD) +meta <- meta %>% + mutate(SV2=NA, .after=SV) +meta[which(meta$sample==46345), 'SV2'] <- unlist(strsplit(meta[which(meta$sample==46345), 'SV'], '/'))[2] +meta[which(meta$sample==46345), 'SV'] <- unlist(strsplit(meta[which(meta$sample==46345), 'SV'], '/'))[1] + +# 2 OPRD >> OPRD2, etc. + # first lapply takes what is after the space = OPRD or OPRI + # second lapply takes what is before the space = 2, 1, ... +meta$SV <- paste0(lapply(strsplit(meta$SV, ' '), function(i) {i[2]}), + lapply(strsplit(meta$SV, ' '), function(i) {i[1]})) +# the NA above become 'NANA', put them back to NA +meta$SV[which(meta$SV=='NANA')] <- NA + +# same for SV2 +meta$SV2 <- paste0(lapply(strsplit(meta$SV2, ' '), function(i) {i[2]}), + lapply(strsplit(meta$SV2, ' '), function(i) {i[1]})) +meta$SV2[which(meta$SV2=='NANA')] <- NA + + + + +# import promoter VCFs ---------------------------------------------------- + +prosv <- as.data.frame(matrix(ncol=11, nrow=0)) + + +# first import regulatory region amplicon calls + # files finish by _promoterSnif.vcf +folder <- here('SVs_sniffles', 'vcf') + +# find indices in list.files of the promoter (regulatory region) VCFs +proinds <- which(unlist(lapply(strsplit(list.files(folder), '_'), function(f){f[2]})) == 'promoterSnif.vcf') # promoter indices +profp <- list.files(folder, full.names=TRUE)[proinds] # promoter full paths + +for (v in 1:length(profp)) { + + path <- profp[v] + pdg <- strsplit(list.files(folder)[proinds][v], '_')[[1]][1] + cat('\t \t \t \t >>> Sample #', pdg, '\n') + + ok <- try(read.table(path)) + + if (!inherits(ok, 'try-error')) { # if no error, read the file; if error, skip to the next one + tmp <- read.table((path)) + tmp <- cbind(rep(pdg, nrow(tmp)), tmp) # add sample where calls came from + prosv <- rbind(prosv, tmp) + } + +} +# add source as first column +prosv <- cbind('promoter', prosv) + + + + +# import genebody VCFs ---------------------------------------------------- + +gbsv <- as.data.frame(matrix(ncol=11, nrow=0)) + + +# second import genebody amplicon calls + # files finish by _bodySnif.vcf + +# find indices in list.files of the genebody VCFs +gbinds <- which(unlist(lapply(strsplit(list.files(folder), '_'), function(f){f[2]})) == 'bodySnif.vcf') # genebody indices +gbfp <- list.files(folder, full.names=TRUE)[gbinds] # genebody full paths + +for (v in 1:length(gbfp)) { + + path <- gbfp[v] + pdg <- strsplit(list.files(folder)[gbinds][v], '_')[[1]][1] + cat('\t \t \t \t >>> Sample #', pdg, '\n') + + ok <- try(read.table(path)) + + if (!inherits(ok, 'try-error')) { # if no error, read the file; if error, skip to the next one + tmp <- read.table((path)) + tmp <- cbind(rep(pdg, nrow(tmp)), tmp) # add sample where calls came from + gbsv <- rbind(gbsv, tmp) + } + +} +# add source as first column +gbsv <- cbind('genebody', gbsv) + + +# stick together both +colnames(prosv) <- sprintf('V%i', 1:ncol(prosv)) +colnames(gbsv) <- sprintf('V%i', 1:ncol(gbsv)) + +sv <- rbind(gbsv, prosv) + + + +# format ------------------------------------------------------------------ + +# column 10 is everything crammed; split in multiple columns +colsplitall <- as.data.frame(t(apply(sv, 1, function(row){ + tmp <- unlist(strsplit(row[10], ';')) + # PRECISE/IMPRECISE is different + # as.data.frame(t(c(tmp[1], as.character(lapply(sapply(tmp[2:length(tmp)], strsplit, '='), function(i) i[2]))))) + colsplit <- c(tmp[1], as.character(lapply(sapply(tmp[2:length(tmp)], strsplit, '='), function(i) i[2]))) + return(colsplit) +}))) + +sv <- cbind(sv,colsplitall) + +colnames(sv) <- c('source', + 'sample', + 'chr', + 'pos', + 'id', + 'ref', + 'alt', + 'qual', + 'filter', + 'info', + 'format_nexttag', + 'geno_readsRef_readsAlt', + 'breakpoints_confidence', + 'svmethod', + 'chr2', + 'end', + 'std_quant_start', + 'std_quant_stop', + 'kurtosis_quant_start', + 'kurtosis_quant_stop', + 'svtype', + 'subtype', + 'svlen', + 'strands', + 'strands2', + 're', + 'ref_strand', + 'strandbias_pval', + 'af') + +# now delete info column +sv$info <- NULL + +# allele frequency column is stored as character, should be numeric +sv$af <- as.numeric(sv$af) +# same with strandbias_pval +sv$strandbias_pval <- as.numeric(sv$strandbias_pval) + + + + +# take only calls in sequenced window ------------------------------------- + +cat('\t \t \t \t >>> Total number of calls:', nrow(sv), 'calls \n') + +# take only calls in PRNP genomic region +# earliest possible position +left <- 4685060 +# latest possible position +right <- 4701756 + +svp <- subset(sv, pos>left & pos>> After filter = only PRNP genomic window:', nrow(svp), 'calls \n') + + + + +# look at calls in regulatory region amplicon ----------------------------- +# i.e. 5' amplicon + +prosv <- subset(svp, source=='promoter') + +# filter them +cat('\t \t \t \t >>> Before filtering:', nrow(prosv), 'calls \n') + +# filter based on allele frequency +# minimum = 10% +prosvf <- subset(prosv, af>0.10) + +cat('\t \t \t \t >>> After filter = Allele Frequency > 0.10:', nrow(prosvf), 'calls \n') + + + + +# look at calls in genebody amplicon -------------------------------------- + +gbsv <- subset(svp, source=='genebody') + +# filter them +cat('\t \t \t \t >>> Before filtering:', nrow(gbsv), 'calls \n') + +# filter based on allele frequency +# minimum = 10% +gbsvf <- subset(gbsv, af>0.10) + +cat('\t \t \t \t >>> After filter = Allele Frequency > 0.10:', nrow(gbsvf), 'calls \n') + + +# For each mutated OPR sample, is there at least one call? +pdgopr <- meta[!is.na(meta$SV), 'sample'] # PDG which have an OPR mutation +sum(pdgopr %in% unique(gbsvf$sample)) == length(pdgopr) + + +# Note; StrandBias flag is slightly problematic +# if look before filtering, many unique calls get called multiple times +# and as one read can only belong to one call, each call gets a low allele frequency +# it also creates imbalances in strand + + + + +# nice export ------------------------------------------------------------- + +# pool filtered calls +svf <- rbind(prosvf, gbsvf) + +# add some sample information +meta$sample <- as.character(meta$sample) +sve <- meta %>% # SV Export + select(sample, gDNA_tissue, prion_disease, SV) %>% + right_join(., svf, by='sample') + +sve$svlen <- as.numeric(sve$svlen) + +# ! svlen does not always match the length of the inserted/deleted sequence +# see https://github.com/fritzsedlazeck/Sniffles/issues/267 +# should look at svlen as this is calculated from multiple reads + +# will add manually in Excel error vs expected SV length + +# export and copy-paste to supplementary +write.xlsx(sve, file=here('SVs_sniffles', 'snifflescallsfilter.xlsx')) + +# also export calls before filtering +write.xlsx(svp, file=here('SVs_sniffles', 'snifflescallsall.xlsx')) \ No newline at end of file diff --git a/SVs_sniffles/vcf/1906_bodySnif.vcf b/SVs_sniffles/vcf/1906_bodySnif.vcf new file mode 100644 index 0000000..156a7ef --- /dev/null +++ b/SVs_sniffles/vcf/1906_bodySnif.vcf @@ -0,0 +1,37 @@ +##fileformat=VCFv4.1 +##source=Sniffles +##fileDate=20210810:52:27 AMef_minus +##contig= +##ALT= +##ALT= +##ALT= +##ALT= +##ALT= +##ALT= +##FILTER= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##FORMAT= +##FORMAT= +##FORMAT= +#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT bamfilt/1906_f.bam +chr20 4699419 0 CAGCCTCATGGTGGTGGCTGGGGGCAGCCCCATGGTGGTGGCTGGGGA N . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4699467;STD_quant_start=0.023796;STD_quant_stop=0.000000;Kurtosis_quant_start=-0.110478;Kurtosis_quant_stop=-0.063398;SVTYPE=DEL;SUPTYPE=AL,NR;SVLEN=-48;STRANDS=+-;STRANDS2=1803,1729,1803,1729;RE=3532;REF_strand=6916,6972;Strandbias_pval=0.187149;AF=0.25432 GT:DR:DV 0/0:10356:3532 diff --git a/SVs_sniffles/vcf/1906_promoterSnif.vcf b/SVs_sniffles/vcf/1906_promoterSnif.vcf new file mode 100644 index 0000000..c31136e --- /dev/null +++ b/SVs_sniffles/vcf/1906_promoterSnif.vcf @@ -0,0 +1,82 @@ +##fileformat=VCFv4.1 +##source=Sniffles +##fileDate=20210811:18:35 AMef_minus +##contig= +##ALT= +##ALT= +##ALT= +##ALT= +##ALT= +##ALT= +##FILTER= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##FORMAT= +##FORMAT= +##FORMAT= +#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT promoterbamfilt/1906_f.bam +chr20 4685224 0 N TTTTTTTTTTT . STRANDBIAS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4685224;STD_quant_start=0.000000;STD_quant_stop=1.174756;Kurtosis_quant_start=385.239881;Kurtosis_quant_stop=2.821965;SVTYPE=INS;SUPTYPE=AL;SVLEN=11;STRANDS=+-;STRANDS2=2301,26,2301,26;RE=2327;REF_strand=52484,30522;Strandbias_pval=0;AF=0.0280341 GT:DR:DV 0/0:80679:2327 +chr20 4685224 1 TTTTTTTTTTT N . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4685235;STD_quant_start=0.000000;STD_quant_stop=0.952277;Kurtosis_quant_start=4.118917;Kurtosis_quant_stop=4.774791;SVTYPE=DEL;SUPTYPE=AL,NR;SVLEN=-11;STRANDS=+-;STRANDS2=198,125,198,125;RE=323;REF_strand=52484,30532;Strandbias_pval=0.488045;AF=0.00389082 GT:DR:DV 0/0:82693:323 +chr20 4685224 2 N TTTTTTTTTTTTTTTTTTTTTTTTTTTTT . STRANDBIAS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4685224;STD_quant_start=0.000000;STD_quant_stop=1.598168;Kurtosis_quant_start=81.342087;Kurtosis_quant_stop=1.136930;SVTYPE=INS;SUPTYPE=AL;SVLEN=17;STRANDS=+-;STRANDS2=305,10,305,10;RE=315;REF_strand=52484,30522;Strandbias_pval=5.72083e-47;AF=0.00379491 GT:DR:DV 0/0:82691:315 +chr20 4685240 3 N TTTTTTTTTTTTTC . STRANDBIAS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4685240;STD_quant_start=0.981307;STD_quant_stop=2.659713;Kurtosis_quant_start=1.402627;Kurtosis_quant_stop=0.596828;SVTYPE=INS;SUPTYPE=AL;SVLEN=12;STRANDS=+-;STRANDS2=48,6,48,6;RE=54;REF_strand=52484,30550;Strandbias_pval=2.99791e-05;AF=0.000650336 GT:DR:DV 0/0:82980:54 +chr20 4685305 4 GCACAATTAAA N . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4685317;STD_quant_start=5.196152;STD_quant_stop=4.618802;Kurtosis_quant_start=-1.755230;Kurtosis_quant_stop=-1.656413;SVTYPE=DEL;SUPTYPE=AL;SVLEN=-12;STRANDS=+-;STRANDS2=15,9,15,9;RE=24;REF_strand=52510,30701;Strandbias_pval=1;AF=0.000288423 GT:DR:DV 0/0:83187:24 +chr20 4685346 5 CCTCCCATCTCAG N . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4685366;STD_quant_start=6.800735;STD_quant_stop=6.298148;Kurtosis_quant_start=-2.092739;Kurtosis_quant_stop=-1.836873;SVTYPE=DEL;SUPTYPE=AL;SVLEN=-20;STRANDS=+-;STRANDS2=14,11,14,11;RE=25;REF_strand=52517,30781;Strandbias_pval=0.535199;AF=0.000300127 GT:DR:DV 0/0:83273:25 +chr20 4685406 6 TCCCAGCAATTTTTTTTATTTTTTG N . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4685422;STD_quant_start=5.795536;STD_quant_stop=4.910972;Kurtosis_quant_start=-1.749772;Kurtosis_quant_stop=-1.574059;SVTYPE=DEL;SUPTYPE=AL;SVLEN=-16;STRANDS=+-;STRANDS2=25,9,25,9;RE=34;REF_strand=52522,30845;Strandbias_pval=0.219542;AF=0.000407835 GT:DR:DV 0/0:83333:34 +chr20 4685464 7 CTCAAACTCCTGAG N . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4685483;STD_quant_start=8.868081;STD_quant_stop=8.426150;Kurtosis_quant_start=-2.083743;Kurtosis_quant_stop=-1.935720;SVTYPE=DEL;SUPTYPE=AL;SVLEN=-19;STRANDS=+-;STRANDS2=17,11,17,11;RE=28;REF_strand=52522,30926;Strandbias_pval=0.845888;AF=0.000335538 GT:DR:DV 0/0:83420:28 +chr20 4685548 8 TCAACATTCTTAAATCTCTTTCCTTACATGC N . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4685574;STD_quant_start=9.702084;STD_quant_stop=8.209221;Kurtosis_quant_start=-1.887177;Kurtosis_quant_stop=-1.791020;SVTYPE=DEL;SUPTYPE=AL;SVLEN=-26;STRANDS=+-;STRANDS2=27,20,27,20;RE=47;REF_strand=52522,31030;Strandbias_pval=0.452936;AF=0.000562524 GT:DR:DV 0/0:83505:47 +chr20 4685625 9 CCCCAGGGCATG N . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4685641;STD_quant_start=5.440588;STD_quant_stop=4.979960;Kurtosis_quant_start=-1.334366;Kurtosis_quant_stop=-1.047518;SVTYPE=DEL;SUPTYPE=AL;SVLEN=-16;STRANDS=+-;STRANDS2=8,8,8,8;RE=16;REF_strand=52524,31133;Strandbias_pval=0.308728;AF=0.000191257 GT:DR:DV 0/0:83641:16 +chr20 4685660 10 N AAAAAAAAAAAAA . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4685665;STD_quant_start=7.893035;STD_quant_stop=5.282045;Kurtosis_quant_start=-0.867276;Kurtosis_quant_stop=-0.871043;SVTYPE=INS;SUPTYPE=AL;SVLEN=11;STRANDS=+-;STRANDS2=10,6,10,6;RE=16;REF_strand=52524,31178;Strandbias_pval=1;AF=0.000191154 GT:DR:DV 0/0:83686:16 +chr20 4685687 11 AGATCCCCCTCCC N . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4685704;STD_quant_start=7.003967;STD_quant_stop=6.159906;Kurtosis_quant_start=-1.658256;Kurtosis_quant_stop=-1.661903;SVTYPE=DEL;SUPTYPE=AL;SVLEN=-17;STRANDS=+-;STRANDS2=17,20,17,20;RE=37;REF_strand=52524,31230;Strandbias_pval=0.0410911;AF=0.00044177 GT:DR:DV 0/0:83717:37 +chr20 4685775 12 CAAGAACACACCAC N . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4685794;STD_quant_start=8.029551;STD_quant_stop=8.920703;Kurtosis_quant_start=-1.887440;Kurtosis_quant_stop=-2.016656;SVTYPE=DEL;SUPTYPE=AL,NR;SVLEN=-19;STRANDS=+-;STRANDS2=18,21,18,21;RE=39;REF_strand=52524,31371;Strandbias_pval=0.0455893;AF=0.000464867 GT:DR:DV 0/0:83856:39 +chr20 4685835 13 N TTTTTTTTTTTTTTTTTTTT . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4685839;STD_quant_start=0.342997;STD_quant_stop=4.485270;Kurtosis_quant_start=-1.487259;Kurtosis_quant_stop=-1.636023;SVTYPE=INS;SUPTYPE=AL;SVLEN=16;STRANDS=+-;STRANDS2=29,6,29,6;RE=35;REF_strand=52524,31448;Strandbias_pval=0.013569;AF=0.000416806 GT:DR:DV 0/0:83937:35 +chr20 4685844 14 CGCATTTTTCT N . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4685859;STD_quant_start=5.358571;STD_quant_stop=5.725881;Kurtosis_quant_start=-1.928302;Kurtosis_quant_stop=-1.984070;SVTYPE=DEL;SUPTYPE=AL;SVLEN=-15;STRANDS=+-;STRANDS2=21,8,21,8;RE=29;REF_strand=52524,31468;Strandbias_pval=0.338962;AF=0.000345271 GT:DR:DV 0/0:83963:29 +chr20 4685915 15 GAAGGAAGGAACAG N . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4685933;STD_quant_start=4.024922;STD_quant_stop=4.049691;Kurtosis_quant_start=-1.257180;Kurtosis_quant_stop=-0.442343;SVTYPE=DEL;SUPTYPE=AL;SVLEN=-18;STRANDS=+-;STRANDS2=7,10,7,10;RE=17;REF_strand=52512,31587;Strandbias_pval=0.0816573;AF=0.000202143 GT:DR:DV 0/0:84082:17 +chr20 4685942 16 GTCCTTTCTAC N . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4685956;STD_quant_start=3.214550;STD_quant_stop=4.974937;Kurtosis_quant_start=-1.790616;Kurtosis_quant_stop=-0.788844;SVTYPE=DEL;SUPTYPE=AL;SVLEN=-14;STRANDS=+-;STRANDS2=17,8,17,8;RE=25;REF_strand=52500,31649;Strandbias_pval=0.681472;AF=0.000297092 GT:DR:DV 0/0:84124:25 +chr20 4686075 17 CCTCATTCCTGAG N . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4686089;STD_quant_start=6.621933;STD_quant_stop=6.920983;Kurtosis_quant_start=-1.521178;Kurtosis_quant_stop=-1.582769;SVTYPE=DEL;SUPTYPE=AL;SVLEN=-14;STRANDS=+-;STRANDS2=28,13,28,13;RE=41;REF_strand=51714,31878;Strandbias_pval=0.426525;AF=0.000490478 GT:DR:DV 0/0:83551:41 +chr20 4686188 18 AGCGATGGCACCCGCA N . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4686208;STD_quant_start=4.230839;STD_quant_stop=5.932959;Kurtosis_quant_start=-0.247055;Kurtosis_quant_stop=-0.199179;SVTYPE=DEL;SUPTYPE=AL;SVLEN=-20;STRANDS=+-;STRANDS2=10,6,10,6;RE=16;REF_strand=51026,32059;Strandbias_pval=1;AF=0.000192574 GT:DR:DV 0/0:83069:16 +chr20 4686249 19 N TTTTTTTTTTTTT . STRANDBIAS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4686249;STD_quant_start=3.370999;STD_quant_stop=5.368257;Kurtosis_quant_start=-1.462589;Kurtosis_quant_stop=-1.328548;SVTYPE=INS;SUPTYPE=AL;SVLEN=13;STRANDS=+-;STRANDS2=20,3,20,3;RE=23;REF_strand=50662,32152;Strandbias_pval=0.00981351;AF=0.000277731 GT:DR:DV 0/0:82791:23 +chr20 4686227 20 GTTCAAGCGAATCTCA N . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4686244;STD_quant_start=4.232808;STD_quant_stop=6.041523;Kurtosis_quant_start=-1.958216;Kurtosis_quant_stop=-1.414644;SVTYPE=DEL;SUPTYPE=AL;SVLEN=-17;STRANDS=+-;STRANDS2=15,10,15,10;RE=25;REF_strand=50781,32129;Strandbias_pval=1;AF=0.000301532 GT:DR:DV 0/0:82885:25 +chr20 4686341 21 GCGCCGGGCCGCGC N . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4686361;STD_quant_start=7.010980;STD_quant_stop=8.246211;Kurtosis_quant_start=-2.163114;Kurtosis_quant_stop=-1.991376;SVTYPE=DEL;SUPTYPE=AL;SVLEN=-20;STRANDS=+-;STRANDS2=12,15,12,15;RE=27;REF_strand=49886,32303;Strandbias_pval=0.113222;AF=0.000328511 GT:DR:DV 0/0:82162:27 +chr20 4686401 22 TTCCCCGCCCCG N . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4686416;STD_quant_start=6.310165;STD_quant_stop=6.988627;Kurtosis_quant_start=-1.258671;Kurtosis_quant_stop=-1.273216;SVTYPE=DEL;SUPTYPE=AL,NR;SVLEN=-15;STRANDS=+-;STRANDS2=42,47,42,47;RE=89;REF_strand=49375,32403;Strandbias_pval=0.0125015;AF=0.00108831 GT:DR:DV 0/0:81689:89 +chr20 4686486 23 CTTCTCCTCTCCT N . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4686501;STD_quant_start=2.722456;STD_quant_stop=4.190325;Kurtosis_quant_start=0.602142;Kurtosis_quant_stop=-1.803183;SVTYPE=DEL;SUPTYPE=AL;SVLEN=-15;STRANDS=+-;STRANDS2=50,19,50,19;RE=69;REF_strand=48771,32600;Strandbias_pval=0.0364332;AF=0.000847968 GT:DR:DV 0/0:81302:69 +chr20 4686614 24 GGGCGGGGTCG N . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4686626;STD_quant_start=2.408319;STD_quant_stop=2.626785;Kurtosis_quant_start=-0.155253;Kurtosis_quant_stop=4.788071;SVTYPE=DEL;SUPTYPE=AL;SVLEN=-12;STRANDS=+-;STRANDS2=11,2,11,2;RE=13;REF_strand=47945,32951;Strandbias_pval=0.0883455;AF=0.0001607 GT:DR:DV 0/0:80883:13 +chr20 4686624 25 N GTGTGTCTGTAGAGGACCC . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4686633;STD_quant_start=8.749026;STD_quant_stop=9.070431;Kurtosis_quant_start=-1.983103;Kurtosis_quant_stop=-1.939858;SVTYPE=INS;SUPTYPE=AL;SVLEN=11;STRANDS=+-;STRANDS2=14,9,14,9;RE=23;REF_strand=47927,32998;Strandbias_pval=1;AF=0.000284214 GT:DR:DV 0/0:80902:23 +chr20 4686637 26 GGAGGGGCCGG N . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4686648;STD_quant_start=4.264014;STD_quant_stop=5.225230;Kurtosis_quant_start=-1.435354;Kurtosis_quant_stop=-1.485156;SVTYPE=DEL;SUPTYPE=AL;SVLEN=-11;STRANDS=+-;STRANDS2=31,35,31,35;RE=66;REF_strand=47888,33028;Strandbias_pval=0.0457001;AF=0.000815661 GT:DR:DV 0/0:80850:66 +chr20 4686880 27 CCGGGAGGGCCGC N . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4686898;STD_quant_start=3.503245;STD_quant_stop=1.906925;Kurtosis_quant_start=0.777437;Kurtosis_quant_stop=-0.025594;SVTYPE=DEL;SUPTYPE=AL,NR;SVLEN=-18;STRANDS=+-;STRANDS2=9,14,9,14;RE=23;REF_strand=46701,33610;Strandbias_pval=0.0888883;AF=0.000286387 GT:DR:DV 0/0:80288:23 +chr20 4686928 28 GGCGCCTGGGGGCC N . STRANDBIAS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4686944;STD_quant_start=6.132790;STD_quant_stop=5.787918;Kurtosis_quant_start=-1.841141;Kurtosis_quant_stop=-1.732044;SVTYPE=DEL;SUPTYPE=AL;SVLEN=-16;STRANDS=+-;STRANDS2=23,50,23,50;RE=73;REF_strand=46463,33752;Strandbias_pval=7.25266e-06;AF=0.000910054 GT:DR:DV 0/0:80142:73 +chr20 4686960 29 CCGCCCGTTGGCCGCCCCTCGGA N . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4686986;STD_quant_start=3.717282;STD_quant_stop=7.868233;Kurtosis_quant_start=-1.721494;Kurtosis_quant_stop=-0.570546;SVTYPE=DEL;SUPTYPE=AL,NR;SVLEN=-26;STRANDS=+-;STRANDS2=19,4,19,4;RE=23;REF_strand=46201,33889;Strandbias_pval=0.0185721;AF=0.000287177 GT:DR:DV 0/0:80067:23 +chr20 4686965 30 N GGGTGAAGCGCCCTT . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4686969;STD_quant_start=6.244998;STD_quant_stop=6.107373;Kurtosis_quant_start=-1.073699;Kurtosis_quant_stop=-0.974290;SVTYPE=INS;SUPTYPE=AL;SVLEN=11;STRANDS=+-;STRANDS2=13,2,13,2;RE=15;REF_strand=46196,33876;Strandbias_pval=0.0330288;AF=0.000187331 GT:DR:DV 0/0:80057:15 +chr20 4687009 31 CCCTTGGCAAGGCCTGGCG N . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4687032;STD_quant_start=7.304108;STD_quant_stop=8.608136;Kurtosis_quant_start=-1.756017;Kurtosis_quant_stop=-1.833737;SVTYPE=DEL;SUPTYPE=AL,NR;SVLEN=-23;STRANDS=+-;STRANDS2=26,15,26,15;RE=41;REF_strand=46027,34016;Strandbias_pval=0.528248;AF=0.000512225 GT:DR:DV 0/0:80002:41 +chr20 4687066 32 CCGGGGGAGTT N . STRANDBIAS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4687087;STD_quant_start=5.493503;STD_quant_stop=5.843189;Kurtosis_quant_start=-1.142782;Kurtosis_quant_stop=-1.597561;SVTYPE=DEL;SUPTYPE=AL;SVLEN=-21;STRANDS=+-;STRANDS2=17,40,17,40;RE=57;REF_strand=45871,34179;Strandbias_pval=3.90104e-05;AF=0.000712055 GT:DR:DV 0/0:79993:57 +chr20 4687202 33 CCACCGCCTGGAGAAGCGGC N . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4687222;STD_quant_start=8.276473;STD_quant_stop=7.197222;Kurtosis_quant_start=-0.520518;Kurtosis_quant_stop=0.132905;SVTYPE=DEL;SUPTYPE=AL;SVLEN=-20;STRANDS=+-;STRANDS2=12,3,12,3;RE=15;REF_strand=45483,34371;Strandbias_pval=0.114682;AF=0.000187843 GT:DR:DV 0/0:79839:15 +chr20 4687309 34 GGGCGGGGAGAGAGGAGCTGCAGGTCTGCGGCCTGGCCCCA N . PASS IMPRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4687347;STD_quant_start=13.319159;STD_quant_stop=5.234501;Kurtosis_quant_start=-1.440658;Kurtosis_quant_stop=-0.479947;SVTYPE=DEL;SUPTYPE=AL;SVLEN=-38;STRANDS=+-;STRANDS2=6,9,6,9;RE=15;REF_strand=44922,34372;Strandbias_pval=0.204291;AF=0.000189169 GT:DR:DV 0/0:79279:15 +chr20 4687590 35 N TTTTTTTTTTTTTTTTT . STRANDBIAS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4687590;STD_quant_start=0.000000;STD_quant_stop=1.905159;Kurtosis_quant_start=0.170747;Kurtosis_quant_stop=-0.723862;SVTYPE=INS;SUPTYPE=AL;SVLEN=11;STRANDS=+-;STRANDS2=53,2,53,2;RE=55;REF_strand=44312,34370;Strandbias_pval=2.06256e-11;AF=0.000699016 GT:DR:DV 0/0:78627:55 +chr20 4687605 36 CGCAATTCCACCA N . PASS IMPRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4687627;STD_quant_start=10.625193;STD_quant_stop=8.391725;Kurtosis_quant_start=-2.118877;Kurtosis_quant_stop=-1.828242;SVTYPE=DEL;SUPTYPE=AL;SVLEN=-22;STRANDS=+-;STRANDS2=19,19,19,19;RE=38;REF_strand=44267,34370;Strandbias_pval=0.513525;AF=0.000483233 GT:DR:DV 0/0:78599:38 +chr20 4687656 37 TCCGTTTTTGTTTCCT N . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4687672;STD_quant_start=6.392704;STD_quant_stop=7.852813;Kurtosis_quant_start=-1.312808;Kurtosis_quant_stop=-1.356638;SVTYPE=DEL;SUPTYPE=AL,NR;SVLEN=-16;STRANDS=+-;STRANDS2=18,13,18,13;RE=31;REF_strand=44185,34370;Strandbias_pval=0.858935;AF=0.000394628 GT:DR:DV 0/0:78524:31 +chr20 4687727 38 CTTCATGGCCGC N . STRANDBIAS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4687742;STD_quant_start=1.607275;STD_quant_stop=3.937004;Kurtosis_quant_start=0.528793;Kurtosis_quant_stop=-1.607584;SVTYPE=DEL;SUPTYPE=AL,NR;SVLEN=-15;STRANDS=+-;STRANDS2=21,3,21,3;RE=24;REF_strand=44058,34370;Strandbias_pval=0.00157461;AF=0.000306013 GT:DR:DV 0/0:78404:24 +chr20 4687786 39 GCAGTTCCCCATATGATTTGAAG N . PASS IMPRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4687810;STD_quant_start=9.125057;STD_quant_stop=10.099505;Kurtosis_quant_start=-1.579302;Kurtosis_quant_stop=-1.788914;SVTYPE=DEL;SUPTYPE=AL;SVLEN=-24;STRANDS=+-;STRANDS2=17,14,17,14;RE=31;REF_strand=43926,34370;Strandbias_pval=1;AF=0.000395933 GT:DR:DV 0/0:78265:31 +chr20 4687919 40 GAACAGGGAATTGGATAAATATGTT N . PASS IMPRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4687952;STD_quant_start=11.850633;STD_quant_stop=13.198011;Kurtosis_quant_start=-2.096931;Kurtosis_quant_stop=-2.062447;SVTYPE=DEL;SUPTYPE=AL;SVLEN=-33;STRANDS=+-;STRANDS2=15,18,15,18;RE=33;REF_strand=43568,34364;Strandbias_pval=0.292623;AF=0.000423446 GT:DR:DV 0/0:77899:33 +chr20 4687973 41 N . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4687990;STD_quant_start=4.358899;STD_quant_stop=4.949747;Kurtosis_quant_start=-1.087818;Kurtosis_quant_stop=-1.147281;SVTYPE=DEL;SUPTYPE=AL;SVLEN=-17;STRANDS=+-;STRANDS2=11,5,11,5;RE=16;REF_strand=43288,34354;Strandbias_pval=0.326835;AF=0.000206074 GT:DR:DV 0/0:77626:16 +chr20 4688011 42 N AAAAAAACAAAAAA . STRANDBIAS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4688014;STD_quant_start=0.000000;STD_quant_stop=2.323790;Kurtosis_quant_start=1.659141;Kurtosis_quant_stop=-0.923074;SVTYPE=INS;SUPTYPE=AL;SVLEN=11;STRANDS=+-;STRANDS2=2,13,2,13;RE=15;REF_strand=42922,34273;Strandbias_pval=0.00109773;AF=0.000194313 GT:DR:DV 0/0:77180:15 +chr20 28640748 43 CTTCATTTGACCTCACTTACTTCTTTGAATGCCTTCTCTAAATCAGTCCCTCTGAGGCAGTGGGGAT N . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=28640815;STD_quant_start=5.375872;STD_quant_stop=9.038805;Kurtosis_quant_start=-1.028686;Kurtosis_quant_stop=-1.111050;SVTYPE=DEL;SUPTYPE=AL;SVLEN=-67;STRANDS=+-;STRANDS2=4,10,4,10;RE=14;REF_strand=12,22;Strandbias_pval=0.745984;AF=0.411765 GT:DR:DV 0/1:20:14 +chr20 28640917 44 N TCTCCCTTTCTCTTTCTTTTTCTTTTCTTTCTTTCTTTTTT . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=28640918;STD_quant_start=5.431390;STD_quant_stop=3.674235;Kurtosis_quant_start=1.346459;Kurtosis_quant_stop=0.952446;SVTYPE=INS;SUPTYPE=AL;SVLEN=39;STRANDS=+-;STRANDS2=6,9,6,9;RE=15;REF_strand=12,22;Strandbias_pval=0.758813;AF=0.441176 GT:DR:DV 0/1:19:15 +chr20 28641119 45 N CCCTTCCTTCCTTCCTTCCTTCCT . PASS IMPRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=28641123;STD_quant_start=12.421755;STD_quant_stop=11.713240;Kurtosis_quant_start=0.578837;Kurtosis_quant_stop=-0.354907;SVTYPE=INS;SUPTYPE=AL;SVLEN=23;STRANDS=+-;STRANDS2=4,6,4,6;RE=10;REF_strand=12,22;Strandbias_pval=1;AF=0.294118 GT:DR:DV 0/0:24:10 diff --git a/SVs_sniffles/vcf/42656_bodySnif.vcf b/SVs_sniffles/vcf/42656_bodySnif.vcf new file mode 100644 index 0000000..36d36ea --- /dev/null +++ b/SVs_sniffles/vcf/42656_bodySnif.vcf @@ -0,0 +1,38 @@ +##fileformat=VCFv4.1 +##source=Sniffles +##fileDate=20210810:52:57 AMef_minus +##contig= +##ALT= +##ALT= +##ALT= +##ALT= +##ALT= +##ALT= +##FILTER= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##FORMAT= +##FORMAT= +##FORMAT= +#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT bamfilt/42656_f.bam +chr20 4699380 0 N GGTGGTGGCTTGGGGCAGCCTCATGGTGGTGGCTGGGGGCAGCCTCATGGTGGTGGCTGGGGGCAGCCTCATGGTGGTGGCTGGGGCAGCCTCAT . STRANDBIAS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4699382;STD_quant_start=4.079915;STD_quant_stop=5.511884;Kurtosis_quant_start=-1.388255;Kurtosis_quant_stop=-1.518969;SVTYPE=INS;SUPTYPE=AL;SVLEN=94;STRANDS=+-;STRANDS2=999,1259,999,1259;RE=2258;REF_strand=6098,6384;Strandbias_pval=5.60074e-05;AF=0.1809 GT:DR:DV 0/0:10224:2258 +chr20 4699447 1 N CTCATGGTGGTGGCTGGGGGCAGCCTCATGGTGGTGGCTGGGGGCAGCCTCATGGTGGTGGCTGGGGGCAGCCTCATGGTGGTGGCTGGGGGCAGT . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4699451;STD_quant_start=8.955520;STD_quant_stop=6.626163;Kurtosis_quant_start=-1.717916;Kurtosis_quant_stop=-1.640401;SVTYPE=INS;SUPTYPE=AL;SVLEN=92;STRANDS=+-;STRANDS2=301,295,301,295;RE=596;REF_strand=6098,6384;Strandbias_pval=0.450366;AF=0.0477488 GT:DR:DV 0/0:11886:596 diff --git a/SVs_sniffles/vcf/42656_promoterSnif.vcf b/SVs_sniffles/vcf/42656_promoterSnif.vcf new file mode 100644 index 0000000..ee83513 --- /dev/null +++ b/SVs_sniffles/vcf/42656_promoterSnif.vcf @@ -0,0 +1,36 @@ +##fileformat=VCFv4.1 +##source=Sniffles +##fileDate=20210811:19:01 AMef_minus +##contig= +##ALT= +##ALT= +##ALT= +##ALT= +##ALT= +##ALT= +##FILTER= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##FORMAT= +##FORMAT= +##FORMAT= +#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT promoterbamfilt/42656_f.bam diff --git a/SVs_sniffles/vcf/43706_bodySnif.vcf b/SVs_sniffles/vcf/43706_bodySnif.vcf new file mode 100644 index 0000000..5cc95bb --- /dev/null +++ b/SVs_sniffles/vcf/43706_bodySnif.vcf @@ -0,0 +1,38 @@ +##fileformat=VCFv4.1 +##source=Sniffles +##fileDate=20210810:53:16 AMef_minus +##contig= +##ALT= +##ALT= +##ALT= +##ALT= +##ALT= +##ALT= +##FILTER= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##FORMAT= +##FORMAT= +##FORMAT= +#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT bamfilt/43706_f.bam +chr20 4699380 0 N GGTGGTGGCTGGGGGCAGCCTCATGTGGTGGCTGGGGCAGCCTGGCTGGTGGTGGCTGGGGGCAGCCTCATGGTGGTGGCTGGGGGCAGCCTTCAT . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4699381;STD_quant_start=4.242452;STD_quant_stop=3.873811;Kurtosis_quant_start=-1.020108;Kurtosis_quant_stop=-1.162469;SVTYPE=INS;SUPTYPE=AL;SVLEN=95;STRANDS=+-;STRANDS2=1116,1381,1116,1381;RE=2497;REF_strand=7490,9296;Strandbias_pval=0.948404;AF=0.148755 GT:DR:DV 0/0:14289:2497 +chr20 4699439 1 N GGGCAGCCTCATGGTGGTGGCTGGGGGCAGCCTCATGGTGGTGGCTGGGGGCAGCCTCGTGGTGGTGGCTGGGGGCAGCCTCATGGTGGTGGCT . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4699439;STD_quant_start=3.997620;STD_quant_stop=4.614574;Kurtosis_quant_start=-1.404082;Kurtosis_quant_stop=-1.247775;SVTYPE=INS;SUPTYPE=AL;SVLEN=95;STRANDS=+-;STRANDS2=653,714,653,714;RE=1367;REF_strand=7490,9296;Strandbias_pval=0.0254749;AF=0.0814369 GT:DR:DV 0/0:15419:1367 diff --git a/SVs_sniffles/vcf/43706_promoterSnif.vcf b/SVs_sniffles/vcf/43706_promoterSnif.vcf new file mode 100644 index 0000000..ccd7e4a --- /dev/null +++ b/SVs_sniffles/vcf/43706_promoterSnif.vcf @@ -0,0 +1,38 @@ +##fileformat=VCFv4.1 +##source=Sniffles +##fileDate=20210811:19:01 AMef_minus +##contig= +##ALT= +##ALT= +##ALT= +##ALT= +##ALT= +##ALT= +##FILTER= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##FORMAT= +##FORMAT= +##FORMAT= +#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT promoterbamfilt/43706_f.bam +chr20 4685224 0 N TTTTTTTTTTT . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4685226;STD_quant_start=0.000000;STD_quant_stop=2.073644;Kurtosis_quant_start=nan;Kurtosis_quant_stop=1.216210;SVTYPE=INS;SUPTYPE=AL;SVLEN=11;STRANDS=+-;STRANDS2=12,0,12,0;RE=12;REF_strand=450,104;Strandbias_pval=0.136173;AF=0.0216606 GT:DR:DV 0/0:542:12 +chr20 4685224 1 TTTTTTTTTTTTT N . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4685236;STD_quant_start=1.643168;STD_quant_stop=1.483240;Kurtosis_quant_start=2.905162;Kurtosis_quant_stop=3.470738;SVTYPE=DEL;SUPTYPE=AL;SVLEN=-12;STRANDS=+-;STRANDS2=12,2,12,2;RE=14;REF_strand=451,104;Strandbias_pval=1;AF=0.0252252 GT:DR:DV 0/0:541:14 diff --git a/SVs_sniffles/vcf/46345_bodySnif.vcf b/SVs_sniffles/vcf/46345_bodySnif.vcf new file mode 100644 index 0000000..49e9cc6 --- /dev/null +++ b/SVs_sniffles/vcf/46345_bodySnif.vcf @@ -0,0 +1,40 @@ +##fileformat=VCFv4.1 +##source=Sniffles +##fileDate=20210810:53:48 AMef_minus +##contig= +##ALT= +##ALT= +##ALT= +##ALT= +##ALT= +##ALT= +##FILTER= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##FORMAT= +##FORMAT= +##FORMAT= +#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT bamfilt/46345_f.bam +chr20 4699380 0 N GGTGGTGGCCGGGGGCAGCTCAAGGTGGCTGTGGGCAGCCTCACGGTGGTGGCTGGGGGCAGCCCCATGGTGGTGGCTGGGGCAGCCTCTTGCGGTGGCTGGGCAGCCTTCAT . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4699380;STD_quant_start=0.274147;STD_quant_stop=2.697908;Kurtosis_quant_start=-1.161499;Kurtosis_quant_stop=-1.189371;SVTYPE=INS;SUPTYPE=AL;SVLEN=120;STRANDS=+-;STRANDS2=948,968,948,968;RE=1916;REF_strand=6866,7074;Strandbias_pval=0.864571;AF=0.137446 GT:DR:DV 0/0:12024:1916 +chr20 4699449 1 CATGGTGGTGGCTGGGGACAGCCT N . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4699473;STD_quant_start=0.000000;STD_quant_stop=0.000000;Kurtosis_quant_start=2.953050;Kurtosis_quant_stop=2.969102;SVTYPE=DEL;SUPTYPE=AL;SVLEN=-24;STRANDS=+-;STRANDS2=1691,1718,1691,1718;RE=3409;REF_strand=6864,7074;Strandbias_pval=0.716564;AF=0.244583 GT:DR:DV 0/0:10529:3409 +chr20 4699439 2 N GGGGCAGCCCCATGGTGGCGGCTGGGGCAGCCTCATGGTAGCGCTGGGGGCAGCCTCATGGTGGTGGCTGGGGGCAGCCTCATGTGGTGGTGGCTGGGGGCAGCCTCATGGTGGTGCT . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4699439;STD_quant_start=1.928792;STD_quant_stop=2.968586;Kurtosis_quant_start=1.057050;Kurtosis_quant_stop=0.696525;SVTYPE=INS;SUPTYPE=AL;SVLEN=119;STRANDS=+-;STRANDS2=341,332,341,332;RE=673;REF_strand=6864,7074;Strandbias_pval=0.477621;AF=0.0482853 GT:DR:DV 0/0:13265:673 +chr20 4699463 3 N GGGGCAGCCTCATGGTGGTGGCTGGGGGCAGCCTCATGGTGGTGGCTGGGGGCAGCCTCATGGTGGTGGCTGGGGGCAGCCTCATGGTGGTGGCTGGGGGCAGCCCCATGGTGGTGGCTGA . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4699465;STD_quant_start=4.867216;STD_quant_stop=4.941288;Kurtosis_quant_start=-0.967768;Kurtosis_quant_stop=-0.954162;SVTYPE=INS;SUPTYPE=AL;SVLEN=117;STRANDS=+-;STRANDS2=233,257,233,257;RE=490;REF_strand=6864,7074;Strandbias_pval=0.462504;AF=0.0351557 GT:DR:DV 0/0:13448:490 diff --git a/SVs_sniffles/vcf/46345_promoterSnif.vcf b/SVs_sniffles/vcf/46345_promoterSnif.vcf new file mode 100644 index 0000000..dd8e7bb --- /dev/null +++ b/SVs_sniffles/vcf/46345_promoterSnif.vcf @@ -0,0 +1,117 @@ +##fileformat=VCFv4.1 +##source=Sniffles +##fileDate=20210811:19:01 AMef_minus +##contig= +##ALT= +##ALT= +##ALT= +##ALT= +##ALT= +##ALT= +##FILTER= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##FORMAT= +##FORMAT= +##FORMAT= +#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT promoterbamfilt/46345_f.bam +chr20 4685160 0 AGTGATTGGTCCTG N . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4685178;STD_quant_start=4.486090;STD_quant_stop=3.570714;Kurtosis_quant_start=-1.039974;Kurtosis_quant_stop=-0.276154;SVTYPE=DEL;SUPTYPE=AL;SVLEN=-18;STRANDS=+-;STRANDS2=20,29,20,29;RE=49;REF_strand=194271,158522;Strandbias_pval=0.0607836;AF=0.000138892 GT:DR:DV 0/0:352744:49 +chr20 4685224 1 GCTTTTTTTTTTTTTTTTGTAAAGAGACAAAGAGTGAGACAGGGTCTTGGCCTATAGCCC N . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4685287;STD_quant_start=1.190238;STD_quant_stop=6.970175;Kurtosis_quant_start=2.013532;Kurtosis_quant_stop=-1.291079;SVTYPE=DEL;SUPTYPE=AL,NR;SVLEN=-63;STRANDS=+-;STRANDS2=9,15,9,15;RE=24;REF_strand=194346,159362;Strandbias_pval=0.101455;AF=6.78526e-05 GT:DR:DV 0/0:353684:24 +chr20 4685224 2 TTTTTTTTTTTTT N . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4685235;STD_quant_start=0.000000;STD_quant_stop=0.972615;Kurtosis_quant_start=4.636991;Kurtosis_quant_stop=3.952594;SVTYPE=DEL;SUPTYPE=AL,NR;SVLEN=-11;STRANDS=+-;STRANDS2=899,694,899,694;RE=1593;REF_strand=194329,159070;Strandbias_pval=0.256085;AF=0.00450765 GT:DR:DV 0/0:351806:1593 +chr20 4685224 3 N TTTTTTTTTTTTTT . STRANDBIAS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4685224;STD_quant_start=0.000000;STD_quant_stop=1.282464;Kurtosis_quant_start=239.758489;Kurtosis_quant_stop=1.477615;SVTYPE=INS;SUPTYPE=AL;SVLEN=11;STRANDS=+-;STRANDS2=9524,164,9524,164;RE=9688;REF_strand=194328,159018;Strandbias_pval=0;AF=0.0274179 GT:DR:DV 0/0:343658:9688 +chr20 4685224 4 N TTTTTTGATTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT . STRANDBIAS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4685224;STD_quant_start=0.000000;STD_quant_stop=2.659771;Kurtosis_quant_start=-0.969297;Kurtosis_quant_stop=3.578194;SVTYPE=INS;SUPTYPE=AL;SVLEN=21;STRANDS=+-;STRANDS2=229,13,229,13;RE=242;REF_strand=194328,159018;Strandbias_pval=2.26208e-43;AF=0.000684881 GT:DR:DV 0/0:353104:242 +chr20 4685232 5 GCACAATTAAA N . STRANDBIAS IMPRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4685317;STD_quant_start=20.713813;STD_quant_stop=16.473804;Kurtosis_quant_start=-1.958313;Kurtosis_quant_stop=-1.954014;SVTYPE=DEL;SUPTYPE=AL;SVLEN=-85;STRANDS=+-;STRANDS2=118,173,118,173;RE=291;REF_strand=194423,159568;Strandbias_pval=1.14871e-06;AF=0.000822055 GT:DR:DV 0/0:353700:291 +chr20 4685242 6 N TTTTTTTTTTTG . STRANDBIAS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4685242;STD_quant_start=1.088400;STD_quant_stop=3.863040;Kurtosis_quant_start=0.418840;Kurtosis_quant_stop=-0.124710;SVTYPE=INS;SUPTYPE=AL;SVLEN=12;STRANDS=+-;STRANDS2=113,17,113,17;RE=130;REF_strand=194348,159222;Strandbias_pval=6.98857e-15;AF=0.000367678 GT:DR:DV 0/0:353440:130 +chr20 4685353 7 CCTCCCATCTCAG N . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4685370;STD_quant_start=8.070559;STD_quant_stop=8.031189;Kurtosis_quant_start=-1.827976;Kurtosis_quant_stop=-1.861442;SVTYPE=DEL;SUPTYPE=AL;SVLEN=-17;STRANDS=+-;STRANDS2=128,96,128,96;RE=224;REF_strand=194526,160440;Strandbias_pval=0.502348;AF=0.000631046 GT:DR:DV 0/0:354742:224 +chr20 4685412 8 ATTTTTTTTAT N . STRANDBIAS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4685424;STD_quant_start=2.190890;STD_quant_stop=1.813529;Kurtosis_quant_start=0.028931;Kurtosis_quant_stop=0.581031;SVTYPE=DEL;SUPTYPE=AL,NR;SVLEN=-12;STRANDS=+-;STRANDS2=65,26,65,26;RE=91;REF_strand=194531,160894;Strandbias_pval=0.00145267;AF=0.000256032 GT:DR:DV 0/0:355334:91 +chr20 4685413 9 N TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT . STRANDBIAS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4685413;STD_quant_start=0.000000;STD_quant_stop=4.462809;Kurtosis_quant_start=1.129436;Kurtosis_quant_stop=-0.879370;SVTYPE=INS;SUPTYPE=AL;SVLEN=11;STRANDS=+-;STRANDS2=251,38,251,38;RE=289;REF_strand=194530,160856;Strandbias_pval=2.12723e-31;AF=0.0008132 GT:DR:DV 0/0:355097:289 +chr20 4685434 10 TGGGGTCTCACTATGTTGCTCACTCTGGTCTCAAACTCCTGAGCTCAAGCAATCTTCCTGCCTTGGCCT N . PASS IMPRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4685504;STD_quant_start=16.444388;STD_quant_stop=8.713517;Kurtosis_quant_start=-2.062537;Kurtosis_quant_stop=-1.725818;SVTYPE=DEL;SUPTYPE=AL;SVLEN=-70;STRANDS=+-;STRANDS2=72,62,72,62;RE=134;REF_strand=194532,161316;Strandbias_pval=0.86237;AF=0.000376565 GT:DR:DV 0/0:355714:134 +chr20 4685497 11 N CCCATCACCCC . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4685500;STD_quant_start=7.010980;STD_quant_stop=7.136041;Kurtosis_quant_start=-1.565815;Kurtosis_quant_stop=-1.974422;SVTYPE=INS;SUPTYPE=AL;SVLEN=12;STRANDS=+-;STRANDS2=12,14,12,14;RE=26;REF_strand=194532,161524;Strandbias_pval=0.433675;AF=7.30222e-05 GT:DR:DV 0/0:356030:26 +chr20 4685597 12 N TAAAAAAAAAAAAAAAAAAAAAAA . STRANDBIAS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4685620;STD_quant_start=5.860702;STD_quant_stop=8.251482;Kurtosis_quant_start=-1.599504;Kurtosis_quant_stop=-1.497292;SVTYPE=INS;SUPTYPE=AL;SVLEN=11;STRANDS=+-;STRANDS2=16,31,16,31;RE=47;REF_strand=194540,162254;Strandbias_pval=0.00521758;AF=0.000131729 GT:DR:DV 0/0:356747:47 +chr20 4685661 13 N AAAAAAAAAAAAAAAAAAAAAAAA . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4685674;STD_quant_start=3.491060;STD_quant_stop=6.937218;Kurtosis_quant_start=-1.648085;Kurtosis_quant_stop=-1.516827;SVTYPE=INS;SUPTYPE=AL;SVLEN=11;STRANDS=+-;STRANDS2=21,12,21,12;RE=33;REF_strand=194542,162641;Strandbias_pval=0.382454;AF=9.23896e-05 GT:DR:DV 0/0:357150:33 +chr20 4685693 14 ATCCCCCTCCCTCTAA N . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4685710;STD_quant_start=4.711902;STD_quant_stop=6.133202;Kurtosis_quant_start=-1.103803;Kurtosis_quant_stop=-1.006759;SVTYPE=DEL;SUPTYPE=AL,NR;SVLEN=-17;STRANDS=+-;STRANDS2=103,95,103,95;RE=198;REF_strand=194542,162919;Strandbias_pval=0.52096;AF=0.000553907 GT:DR:DV 0/0:357263:198 +chr20 4685753 15 N TGATATATTATCC . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4685761;STD_quant_start=7.951778;STD_quant_stop=9.915024;Kurtosis_quant_start=-1.732539;Kurtosis_quant_stop=-1.789409;SVTYPE=INS;SUPTYPE=AL;SVLEN=11;STRANDS=+-;STRANDS2=31,21,31,21;RE=52;REF_strand=194542,163296;Strandbias_pval=0.488317;AF=0.000145317 GT:DR:DV 0/0:357786:52 +chr20 4685835 16 N CATTTAAAAAAACACACT . STRANDBIAS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4685856;STD_quant_start=3.422614;STD_quant_stop=8.826367;Kurtosis_quant_start=-1.197289;Kurtosis_quant_stop=-1.456433;SVTYPE=INS;SUPTYPE=AL;SVLEN=11;STRANDS=+-;STRANDS2=65,19,65,19;RE=84;REF_strand=194544,163868;Strandbias_pval=1.44966e-05;AF=0.000234367 GT:DR:DV 0/0:358328:84 +chr20 4685919 17 AAGGAAGGAACAGGT N . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4685938;STD_quant_start=3.685833;STD_quant_stop=3.432272;Kurtosis_quant_start=-0.040051;Kurtosis_quant_stop=-0.719719;SVTYPE=DEL;SUPTYPE=AL;SVLEN=-19;STRANDS=+-;STRANDS2=42,41,42,41;RE=83;REF_strand=194533,164395;Strandbias_pval=0.511201;AF=0.000231244 GT:DR:DV 0/0:358845:83 +chr20 4685973 18 ATGTGAAAATTC N . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4685988;STD_quant_start=5.606772;STD_quant_stop=5.131601;Kurtosis_quant_start=-1.809600;Kurtosis_quant_stop=-1.706597;SVTYPE=DEL;SUPTYPE=AL;SVLEN=-15;STRANDS=+-;STRANDS2=42,37,42,37;RE=79;REF_strand=194298,164726;Strandbias_pval=0.910294;AF=0.000220041 GT:DR:DV 0/0:358945:79 +chr20 4686011 19 TTAAGCAAAATTTT N . STRANDBIAS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4686025;STD_quant_start=4.441339;STD_quant_stop=4.671566;Kurtosis_quant_start=0.633469;Kurtosis_quant_stop=0.674781;SVTYPE=DEL;SUPTYPE=AL,NR;SVLEN=-14;STRANDS=+-;STRANDS2=36,67,36,67;RE=103;REF_strand=193920,164972;Strandbias_pval=0.000145131;AF=0.000286994 GT:DR:DV 0/0:358789:103 +chr20 4686046 20 N GGGTTTTTTTTTTTTTTTTT . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4686052;STD_quant_start=4.264681;STD_quant_stop=5.326819;Kurtosis_quant_start=-1.548847;Kurtosis_quant_stop=-0.716798;SVTYPE=INS;SUPTYPE=AL;SVLEN=11;STRANDS=+-;STRANDS2=18,15,18,15;RE=33;REF_strand=193656,165161;Strandbias_pval=1;AF=9.19689e-05 GT:DR:DV 0/0:358784:33 +chr20 4686075 21 CCTCATTCCTGAGC N . STRANDBIAS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4686088;STD_quant_start=5.799562;STD_quant_stop=6.662499;Kurtosis_quant_start=-1.693591;Kurtosis_quant_stop=-1.647126;SVTYPE=DEL;SUPTYPE=AL;SVLEN=-13;STRANDS=+-;STRANDS2=157,95,157,95;RE=252;REF_strand=193371,165369;Strandbias_pval=0.00785324;AF=0.000702459 GT:DR:DV 0/0:358488:252 +chr20 4686105 22 N TTGATTTGTTG . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4686110;STD_quant_start=7.242551;STD_quant_stop=7.428447;Kurtosis_quant_start=-2.007742;Kurtosis_quant_stop=-1.874843;SVTYPE=INS;SUPTYPE=AL;SVLEN=11;STRANDS=+-;STRANDS2=30,15,30,15;RE=45;REF_strand=193185,165540;Strandbias_pval=0.099792;AF=0.000125444 GT:DR:DV 0/0:358680:45 +chr20 4686130 23 TTGGGCCGAATTTCC N . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4686149;STD_quant_start=2.041241;STD_quant_stop=3.041381;Kurtosis_quant_start=0.574109;Kurtosis_quant_stop=0.073390;SVTYPE=DEL;SUPTYPE=AL,NR;SVLEN=-19;STRANDS=+-;STRANDS2=25,23,25,23;RE=48;REF_strand=192932,165721;Strandbias_pval=0.885186;AF=0.000133834 GT:DR:DV 0/0:358605:48 +chr20 4686134 24 N GCAGCTGCCACGCCGCAC . STRANDBIAS IMPRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4686163;STD_quant_start=14.031350;STD_quant_stop=8.838620;Kurtosis_quant_start=-1.791118;Kurtosis_quant_stop=-1.661845;SVTYPE=INS;SUPTYPE=AL;SVLEN=12;STRANDS=+-;STRANDS2=53,13,53,13;RE=66;REF_strand=192835,165775;Strandbias_pval=9.97753e-06;AF=0.000184044 GT:DR:DV 0/0:358544:66 +chr20 4686176 25 GATGGCACCCGCAGGCGG N . STRANDBIAS IMPRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4686212;STD_quant_start=12.957097;STD_quant_stop=10.262465;Kurtosis_quant_start=-1.771379;Kurtosis_quant_stop=-1.913593;SVTYPE=DEL;SUPTYPE=AL,NR;SVLEN=-36;STRANDS=+-;STRANDS2=76,101,76,101;RE=177;REF_strand=192408,166088;Strandbias_pval=0.00513848;AF=0.000493729 GT:DR:DV 0/0:358319:177 +chr20 4686252 26 TTTCCGGTGAC N . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4686266;STD_quant_start=1.809068;STD_quant_stop=2.705214;Kurtosis_quant_start=-0.261273;Kurtosis_quant_stop=0.193154;SVTYPE=DEL;SUPTYPE=AL;SVLEN=-14;STRANDS=+-;STRANDS2=22,22,22,22;RE=44;REF_strand=191673,166493;Strandbias_pval=0.653337;AF=0.000122848 GT:DR:DV 0/0:358122:44 +chr20 4686310 27 GGCCGGCCGCCCGCCGG N . STRANDBIAS IMPRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4686341;STD_quant_start=13.263413;STD_quant_stop=12.671513;Kurtosis_quant_start=-2.094178;Kurtosis_quant_stop=-1.775490;SVTYPE=DEL;SUPTYPE=AL,NR;SVLEN=-31;STRANDS=+-;STRANDS2=144,199,144,199;RE=343;REF_strand=190932,166967;Strandbias_pval=2.85577e-05;AF=0.000958371 GT:DR:DV 0/0:357556:343 +chr20 4686298 28 N CGATTGATGCCGGTACCA . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4686303;STD_quant_start=7.365460;STD_quant_stop=9.239859;Kurtosis_quant_start=-2.071341;Kurtosis_quant_stop=-2.029786;SVTYPE=INS;SUPTYPE=AL;SVLEN=12;STRANDS=+-;STRANDS2=22,11,22,11;RE=33;REF_strand=191161,166780;Strandbias_pval=0.162205;AF=9.2194e-05 GT:DR:DV 0/0:357908:33 +chr20 4686365 29 CCCCGCGCCGA N . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4686376;STD_quant_start=3.712591;STD_quant_stop=4.143268;Kurtosis_quant_start=0.164760;Kurtosis_quant_stop=-0.858535;SVTYPE=DEL;SUPTYPE=AL;SVLEN=-11;STRANDS=+-;STRANDS2=59,62,59,62;RE=121;REF_strand=190457,167283;Strandbias_pval=0.362294;AF=0.000338234 GT:DR:DV 0/0:357619:121 +chr20 4686359 30 GGCCGCGCGGCAATTGGTCCCCGCGCCGACCTCCGCCCGCGAGCGCCGCCGCTTCCCTTCCCCGCCCCGCGTCCCTCCCCCTCGGCCCCGC N . PASS IMPRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4686438;STD_quant_start=10.024969;STD_quant_stop=10.733126;Kurtosis_quant_start=-1.524577;Kurtosis_quant_stop=-1.854485;SVTYPE=DEL;SUPTYPE=AL,NR;SVLEN=-79;STRANDS=+-;STRANDS2=11,10,11,10;RE=21;REF_strand=190190,167475;Strandbias_pval=1;AF=5.87142e-05 GT:DR:DV 0/0:357644:21 +chr20 4686335 31 N GGCGCGAGTACGCTGCGGCGCGC . PASS IMPRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4686345;STD_quant_start=5.990734;STD_quant_stop=11.249691;Kurtosis_quant_start=-1.706172;Kurtosis_quant_stop=-2.054127;SVTYPE=INS;SUPTYPE=AL;SVLEN=11;STRANDS=+-;STRANDS2=20,16,20,16;RE=36;REF_strand=190767,167105;Strandbias_pval=0.867999;AF=0.000100595 GT:DR:DV 0/0:357836:36 +chr20 4686410 32 N GCCGCGCAGGCGCG . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4686423;STD_quant_start=9.888009;STD_quant_stop=8.655004;Kurtosis_quant_start=-2.086708;Kurtosis_quant_stop=-1.793861;SVTYPE=INS;SUPTYPE=AL;SVLEN=11;STRANDS=+-;STRANDS2=19,25,19,25;RE=44;REF_strand=190001,167582;Strandbias_pval=0.226688;AF=0.000123048 GT:DR:DV 0/0:357539:44 +chr20 4686411 33 CCTCGGCCCCG N . STRANDBIAS IMPRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4686437;STD_quant_start=6.538550;STD_quant_stop=10.088034;Kurtosis_quant_start=-1.974552;Kurtosis_quant_stop=-2.011533;SVTYPE=DEL;SUPTYPE=AL;SVLEN=-26;STRANDS=+-;STRANDS2=151,230,151,230;RE=381;REF_strand=189934,167632;Strandbias_pval=1.40662e-07;AF=0.00106554 GT:DR:DV 0/0:357185:381 +chr20 4686452 34 N CGGAGGAGTGG . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4686458;STD_quant_start=4.074310;STD_quant_stop=4.483302;Kurtosis_quant_start=-0.726272;Kurtosis_quant_stop=-1.361922;SVTYPE=INS;SUPTYPE=AL;SVLEN=12;STRANDS=+-;STRANDS2=15,6,15,6;RE=21;REF_strand=189702,167832;Strandbias_pval=0.124704;AF=5.87357e-05 GT:DR:DV 0/0:357513:21 +chr20 4686457 35 GTCGCTGACAGCCGCGGCGCCGCGAGCTTCTCCTCTCCTCACGACCGAGGCAGGTAAACGCCCGGGGTGGGAGGAACGCGGGCGGGGGCAGGGGAGCCGCGGGGGCCG N . PASS IMPRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4686568;STD_quant_start=27.633313;STD_quant_stop=17.717223;Kurtosis_quant_start=-0.961013;Kurtosis_quant_stop=0.913733;SVTYPE=DEL;SUPTYPE=AL;SVLEN=-111;STRANDS=+-;STRANDS2=2,8,2,8;RE=10;REF_strand=189160,168232;Strandbias_pval=0.0539949;AF=2.79805e-05 GT:DR:DV 0/0:357382:10 +chr20 4686486 36 CTTCTCCTCTC N . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4686497;STD_quant_start=5.005674;STD_quant_stop=4.605389;Kurtosis_quant_start=-1.591160;Kurtosis_quant_stop=-1.592667;SVTYPE=DEL;SUPTYPE=AL;SVLEN=-11;STRANDS=+-;STRANDS2=216,243,216,243;RE=459;REF_strand=189369,168043;Strandbias_pval=0.0114868;AF=0.00128423 GT:DR:DV 0/0:356953:459 +chr20 4686503 37 N CCCTTGCCAGCCCGTGG . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4686508;STD_quant_start=4.412549;STD_quant_stop=3.589199;Kurtosis_quant_start=-1.600456;Kurtosis_quant_stop=-1.252360;SVTYPE=INS;SUPTYPE=AL;SVLEN=11;STRANDS=+-;STRANDS2=20,14,20,14;RE=34;REF_strand=189272,168142;Strandbias_pval=0.606954;AF=9.51278e-05 GT:DR:DV 0/0:357380:34 +chr20 4686532 38 N AGGCAGCACATGGCAGGAA . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4686541;STD_quant_start=5.131601;STD_quant_stop=5.552777;Kurtosis_quant_start=-1.790247;Kurtosis_quant_stop=-0.088920;SVTYPE=INS;SUPTYPE=AL;SVLEN=12;STRANDS=+-;STRANDS2=11,14,11,14;RE=25;REF_strand=188910,168364;Strandbias_pval=0.425982;AF=6.99743e-05 GT:DR:DV 0/0:357249:25 +chr20 4686550 39 GGGGGCCGAGT N . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4686571;STD_quant_start=4.002136;STD_quant_stop=3.420651;Kurtosis_quant_start=-0.571571;Kurtosis_quant_stop=-1.184975;SVTYPE=DEL;SUPTYPE=AL,NR;SVLEN=-21;STRANDS=+-;STRANDS2=135,100,135,100;RE=235;REF_strand=188705,168553;Strandbias_pval=0.16984;AF=0.000657788 GT:DR:DV 0/0:357023:235 +chr20 4686565 40 CCGAGTGAGGACC N . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4686614;STD_quant_start=6.579900;STD_quant_stop=9.932147;Kurtosis_quant_start=-1.792978;Kurtosis_quant_stop=-2.019320;SVTYPE=DEL;SUPTYPE=AL;SVLEN=-49;STRANDS=+-;STRANDS2=145,99,145,99;RE=244;REF_strand=188506,168778;Strandbias_pval=0.0399992;AF=0.00068293 GT:DR:DV 0/0:357040:244 +chr20 4686632 41 N ATCTCAAACAGCG . PASS IMPRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4686641;STD_quant_start=9.767292;STD_quant_stop=10.564090;Kurtosis_quant_start=-1.002601;Kurtosis_quant_stop=-1.452132;SVTYPE=INS;SUPTYPE=AL;SVLEN=11;STRANDS=+-;STRANDS2=3,11,3,11;RE=14;REF_strand=188209,169187;Strandbias_pval=0.0288769;AF=3.91722e-05 GT:DR:DV 0/0:357382:14 +chr20 4686637 42 GGGCCGGGGGCT N . STRANDBIAS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4686653;STD_quant_start=5.515998;STD_quant_stop=6.960073;Kurtosis_quant_start=-1.279187;Kurtosis_quant_stop=-1.422206;SVTYPE=DEL;SUPTYPE=AL,NR;SVLEN=-16;STRANDS=+-;STRANDS2=209,280,209,280;RE=489;REF_strand=188140,169269;Strandbias_pval=1.28813e-05;AF=0.00136818 GT:DR:DV 0/0:356920:489 +chr20 4686688 43 N TGAGGGGAGGAGTAT . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4686698;STD_quant_start=7.200146;STD_quant_stop=8.897072;Kurtosis_quant_start=-1.515679;Kurtosis_quant_stop=-1.650649;SVTYPE=INS;SUPTYPE=AL;SVLEN=12;STRANDS=+-;STRANDS2=24,14,24,14;RE=38;REF_strand=187773,169648;Strandbias_pval=0.198425;AF=0.000106317 GT:DR:DV 0/0:357383:38 +chr20 4686758 44 GCGTTGGGGGGCTGGGGGAGCTGGCGGAGCCCCGTTAGGGAGGTCGGTGG N . PASS IMPRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4686816;STD_quant_start=10.251829;STD_quant_stop=16.315637;Kurtosis_quant_start=0.463022;Kurtosis_quant_stop=-0.824845;SVTYPE=DEL;SUPTYPE=AL;SVLEN=-58;STRANDS=+-;STRANDS2=4,7,4,7;RE=11;REF_strand=186939,170304;Strandbias_pval=0.370584;AF=3.07914e-05 GT:DR:DV 0/0:357232:11 +chr20 4686747 45 N CGCGCCCTTCA . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4686759;STD_quant_start=7.443908;STD_quant_stop=6.412304;Kurtosis_quant_start=-1.727172;Kurtosis_quant_stop=-1.788512;SVTYPE=INS;SUPTYPE=AL;SVLEN=11;STRANDS=+-;STRANDS2=22,13,22,13;RE=35;REF_strand=187198,170042;Strandbias_pval=0.239089;AF=9.79734e-05 GT:DR:DV 0/0:357205:35 +chr20 4686839 46 GGGTCCGGCCCAGCGGGCGATCGCTGGCGCCCAGGGAACTCCGGGAGGGCCGCCAGCGGGCTCCGCAGGGCGCGGGGCGGGGAGGGGCGCCTGGGGGCCGCGGGGCTCGCGCTCCCCGCCCGTTG N . PASS IMPRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4686953;STD_quant_start=24.637370;STD_quant_stop=18.601075;Kurtosis_quant_start=-0.341999;Kurtosis_quant_stop=-0.743857;SVTYPE=DEL;SUPTYPE=AL;SVLEN=-114;STRANDS=+-;STRANDS2=2,8,2,8;RE=10;REF_strand=186022,171101;Strandbias_pval=0.0564606;AF=2.80016e-05 GT:DR:DV 0/0:357113:10 +chr20 4686928 47 GGCGCCTGGGGGCCGCGGGGCTCGCGCT N . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4686959;STD_quant_start=9.308013;STD_quant_stop=8.549502;Kurtosis_quant_start=-1.520499;Kurtosis_quant_stop=-1.476198;SVTYPE=DEL;SUPTYPE=AL,NR;SVLEN=-31;STRANDS=+-;STRANDS2=252,280,252,280;RE=532;REF_strand=185613,171417;Strandbias_pval=0.0334139;AF=0.00149007 GT:DR:DV 0/0:356498:532 +chr20 4686953 48 GCGCTCCCCGCCCGTTGGCCGCCCCTCGGAGGCCGAGATCGGGGCCCAGAACGCCCCTTGGCAAGGCCTGGCGCTTCCGCGATGCCCAGAGGGTGCTTGGGGGGA N . PASS IMPRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4687047;STD_quant_start=13.928388;STD_quant_stop=6.700746;Kurtosis_quant_start=-0.455530;Kurtosis_quant_stop=4.544625;SVTYPE=DEL;SUPTYPE=AL,NR;SVLEN=-94;STRANDS=+-;STRANDS2=8,3,8,3;RE=11;REF_strand=185180,171905;Strandbias_pval=0.230116;AF=3.0805e-05 GT:DR:DV 0/0:357074:11 +chr20 4686971 49 N CAATAGCCCTA . STRANDBIAS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4686973;STD_quant_start=4.391550;STD_quant_stop=4.639376;Kurtosis_quant_start=-1.652687;Kurtosis_quant_stop=-1.436993;SVTYPE=INS;SUPTYPE=AL;SVLEN=11;STRANDS=+-;STRANDS2=35,7,35,7;RE=42;REF_strand=185376,171695;Strandbias_pval=3.38433e-05;AF=0.000117624 GT:DR:DV 0/0:357029:42 +chr20 4687018 50 CGCGATGCCCAG N . STRANDBIAS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4687044;STD_quant_start=4.690416;STD_quant_stop=4.140393;Kurtosis_quant_start=-0.891453;Kurtosis_quant_stop=-1.688843;SVTYPE=DEL;SUPTYPE=AL;SVLEN=-26;STRANDS=+-;STRANDS2=43,13,43,13;RE=56;REF_strand=184956,172171;Strandbias_pval=0.000146829;AF=0.000156807 GT:DR:DV 0/0:357071:56 +chr20 4687066 51 GGGGCGCCCGCC N . STRANDBIAS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4687078;STD_quant_start=5.826050;STD_quant_stop=6.114775;Kurtosis_quant_start=-1.542249;Kurtosis_quant_stop=-1.359620;SVTYPE=DEL;SUPTYPE=AL,NR;SVLEN=-12;STRANDS=+-;STRANDS2=142,278,142,278;RE=420;REF_strand=184630,172473;Strandbias_pval=1.90214e-13;AF=0.00117613 GT:DR:DV 0/0:356683:420 +chr20 4687114 52 GCTGCAGCGTTCCTCCCGGGAG N . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4687136;STD_quant_start=4.207137;STD_quant_stop=5.059644;Kurtosis_quant_start=-0.858086;Kurtosis_quant_stop=-1.193472;SVTYPE=DEL;SUPTYPE=AL,NR;SVLEN=-22;STRANDS=+-;STRANDS2=11,6,11,6;RE=17;REF_strand=184222,172850;Strandbias_pval=0.336501;AF=4.76094e-05 GT:DR:DV 0/0:357055:17 +chr20 4687166 53 N AGAAGAAGAAG . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4687166;STD_quant_start=1.032796;STD_quant_stop=1.549193;Kurtosis_quant_start=-0.677505;Kurtosis_quant_stop=2.571238;SVTYPE=INS;SUPTYPE=AL;SVLEN=13;STRANDS=+-;STRANDS2=20,11,20,11;RE=31;REF_strand=183980,173040;Strandbias_pval=0.155516;AF=8.68299e-05 GT:DR:DV 0/0:356989:31 +chr20 4687176 54 GGGGGCTGCAGCCTTGCGGCCGTTGCCACCGCCTGGAGAAGCGGCCCACGCGGACTGACGGGCGGGGGC N . PASS IMPRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4687249;STD_quant_start=7.840068;STD_quant_stop=12.992305;Kurtosis_quant_start=-0.731829;Kurtosis_quant_stop=-1.415690;SVTYPE=DEL;SUPTYPE=AL;SVLEN=-73;STRANDS=+-;STRANDS2=16,14,16,14;RE=30;REF_strand=183645,173042;Strandbias_pval=0.857433;AF=8.41074e-05 GT:DR:DV 0/0:356657:30 +chr20 4687128 55 CCCGGGAGGCGGC N . PASS IMPRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4687177;STD_quant_start=5.519263;STD_quant_stop=12.068202;Kurtosis_quant_start=-1.311903;Kurtosis_quant_stop=-2.098779;SVTYPE=DEL;SUPTYPE=AL,NR;SVLEN=-49;STRANDS=+-;STRANDS2=123,89,123,89;RE=212;REF_strand=184037,172953;Strandbias_pval=0.0634456;AF=0.000593854 GT:DR:DV 0/0:356778:212 +chr20 4687178 56 GGGGCTGCAGCCTTGCGGCC N . PASS IMPRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4687201;STD_quant_start=10.199587;STD_quant_stop=8.288864;Kurtosis_quant_start=-1.973887;Kurtosis_quant_stop=-1.558380;SVTYPE=DEL;SUPTYPE=AL;SVLEN=-23;STRANDS=+-;STRANDS2=110,80,110,80;RE=190;REF_strand=183820,173042;Strandbias_pval=0.0816187;AF=0.000532419 GT:DR:DV 0/0:356672:190 +chr20 4687206 57 N CACCGCCTTGCTGCTA . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4687211;STD_quant_start=5.927338;STD_quant_stop=6.633250;Kurtosis_quant_start=-1.865003;Kurtosis_quant_stop=-1.638624;SVTYPE=INS;SUPTYPE=AL;SVLEN=11;STRANDS=+-;STRANDS2=15,15,15,15;RE=30;REF_strand=183701,173045;Strandbias_pval=1;AF=8.40934e-05 GT:DR:DV 0/0:356716:30 +chr20 4687302 58 GGGAGAGAGGA N . STRANDBIAS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4687320;STD_quant_start=3.359934;STD_quant_stop=2.796297;Kurtosis_quant_start=-0.137968;Kurtosis_quant_stop=2.283488;SVTYPE=DEL;SUPTYPE=AL,NR;SVLEN=-18;STRANDS=+-;STRANDS2=60,106,60,106;RE=166;REF_strand=182816,173044;Strandbias_pval=9.32952e-05;AF=0.000466476 GT:DR:DV 0/0:355694:166 +chr20 4687344 59 N GCAGCCGCCGCGCAGCGCC . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4687353;STD_quant_start=6.320393;STD_quant_stop=8.094833;Kurtosis_quant_start=-1.447862;Kurtosis_quant_stop=-1.873373;SVTYPE=INS;SUPTYPE=AL;SVLEN=11;STRANDS=+-;STRANDS2=17,21,17,21;RE=38;REF_strand=182573,173044;Strandbias_pval=0.423082;AF=0.000106857 GT:DR:DV 0/0:355579:38 +chr20 4687424 60 CCAAGGAACAA N . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4687435;STD_quant_start=1.840407;STD_quant_stop=1.425573;Kurtosis_quant_start=1.094946;Kurtosis_quant_stop=1.167985;SVTYPE=DEL;SUPTYPE=AL;SVLEN=-11;STRANDS=+-;STRANDS2=34,28,34,28;RE=62;REF_strand=182160,173042;Strandbias_pval=0.612749;AF=0.000174549 GT:DR:DV 0/0:355140:62 +chr20 4687390 61 N CCCCCCCCCCCCCCCCCCCCCCCCCC . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4687407;STD_quant_start=2.900304;STD_quant_stop=9.896523;Kurtosis_quant_start=-1.528865;Kurtosis_quant_stop=-1.741966;SVTYPE=INS;SUPTYPE=AL;SVLEN=11;STRANDS=+-;STRANDS2=16,18,16,18;RE=34;REF_strand=182327,173044;Strandbias_pval=0.732111;AF=9.56747e-05 GT:DR:DV 0/0:355337:34 +chr20 4687453 62 N AATAACAAGCAATGTAAGGGTAAT . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4687462;STD_quant_start=8.679478;STD_quant_stop=9.656604;Kurtosis_quant_start=-2.167035;Kurtosis_quant_stop=-2.128160;SVTYPE=INS;SUPTYPE=AL;SVLEN=12;STRANDS=+-;STRANDS2=9,16,9,16;RE=25;REF_strand=182003,173042;Strandbias_pval=0.161151;AF=7.04136e-05 GT:DR:DV 0/0:355020:25 +chr20 4687451 63 TGCGGCAGGCGCCTTCACGTTT N . PASS IMPRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4687501;STD_quant_start=12.738152;STD_quant_stop=13.196638;Kurtosis_quant_start=-1.841515;Kurtosis_quant_stop=-1.960708;SVTYPE=DEL;SUPTYPE=AL;SVLEN=-50;STRANDS=+-;STRANDS2=140,99,140,99;RE=239;REF_strand=181862,173041;Strandbias_pval=0.0235468;AF=0.000673423 GT:DR:DV 0/0:354664:239 +chr20 4687540 64 N CTTTTTTTTTTTT . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4687540;STD_quant_start=0.316228;STD_quant_stop=3.667424;Kurtosis_quant_start=-0.836217;Kurtosis_quant_stop=-1.411385;SVTYPE=INS;SUPTYPE=AL;SVLEN=12;STRANDS=+-;STRANDS2=29,12,29,12;RE=41;REF_strand=181322,173038;Strandbias_pval=0.012423;AF=0.000115702 GT:DR:DV 0/0:354319:41 +chr20 4687540 65 TTTTTAAGGAATTTTTTG N . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4687566;STD_quant_start=3.644531;STD_quant_stop=5.727508;Kurtosis_quant_start=-0.798649;Kurtosis_quant_stop=-1.586164;SVTYPE=DEL;SUPTYPE=AL;SVLEN=-26;STRANDS=+-;STRANDS2=43,50,43,50;RE=93;REF_strand=181237,173038;Strandbias_pval=0.35235;AF=0.000262508 GT:DR:DV 0/0:354182:93 +chr20 4687590 66 N TTTTTTTTTTTTTTTTTT . STRANDBIAS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4687590;STD_quant_start=0.000000;STD_quant_stop=1.620650;Kurtosis_quant_start=-0.017343;Kurtosis_quant_stop=-0.937992;SVTYPE=INS;SUPTYPE=AL;SVLEN=12;STRANDS=+-;STRANDS2=154,13,154,13;RE=167;REF_strand=180892,173036;Strandbias_pval=1.25016e-30;AF=0.000471847 GT:DR:DV 0/0:353761:167 +chr20 4687579 67 AAATAGATTTTTTTTTTAACCT N . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4687606;STD_quant_start=5.970585;STD_quant_stop=5.644391;Kurtosis_quant_start=-1.960062;Kurtosis_quant_stop=-1.223616;SVTYPE=DEL;SUPTYPE=AL,NR;SVLEN=-27;STRANDS=+-;STRANDS2=66,76,66,76;RE=142;REF_strand=180917,173035;Strandbias_pval=0.276197;AF=0.000401184 GT:DR:DV 0/0:353810:142 +chr20 4687656 68 ATCCATCCTCGCCATCGCAGAGCCACAGCTCTCCGTTTTTGTTTCCTAGCCTCCAGATTCTCACACAACACAGTGCAGTTTCACTGCTGTAATGATGAGGATCTTCATGGCCGCGTTA N . PASS IMPRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4687751;STD_quant_start=8.087027;STD_quant_stop=17.303179;Kurtosis_quant_start=-1.095322;Kurtosis_quant_stop=-1.948742;SVTYPE=DEL;SUPTYPE=AL,NR;SVLEN=-95;STRANDS=+-;STRANDS2=8,6,8,6;RE=14;REF_strand=180121,173029;Strandbias_pval=0.791114;AF=3.96432e-05 GT:DR:DV 0/0:353136:14 +chr20 4687660 69 N TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT . PASS IMPRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4687695;STD_quant_start=11.019214;STD_quant_stop=9.382881;Kurtosis_quant_start=-1.782690;Kurtosis_quant_stop=-1.873631;SVTYPE=INS;SUPTYPE=AL;SVLEN=11;STRANDS=+-;STRANDS2=35,18,35,18;RE=53;REF_strand=180323,173029;Strandbias_pval=0.0382994;AF=0.000149992 GT:DR:DV 0/0:353299:53 +chr20 4687768 70 N TTTTTTTTTTT . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4687778;STD_quant_start=5.826186;STD_quant_stop=8.246211;Kurtosis_quant_start=-1.404747;Kurtosis_quant_stop=-1.956054;SVTYPE=INS;SUPTYPE=AL;SVLEN=11;STRANDS=+-;STRANDS2=23,13,23,13;RE=36;REF_strand=179602,173025;Strandbias_pval=0.134905;AF=0.000102091 GT:DR:DV 0/0:352591:36 +chr20 4687806 71 CGTTTCCTTAGGGAA N . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4687817;STD_quant_start=4.675162;STD_quant_stop=5.234501;Kurtosis_quant_start=-1.180862;Kurtosis_quant_stop=-1.177229;SVTYPE=DEL;SUPTYPE=AL,NR;SVLEN=-11;STRANDS=+-;STRANDS2=33,38,33,38;RE=71;REF_strand=179269,173022;Strandbias_pval=0.478205;AF=0.000201538 GT:DR:DV 0/0:352220:71 +chr20 4687847 72 N AGAAAAAGAAAG . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4687848;STD_quant_start=5.883484;STD_quant_stop=6.158172;Kurtosis_quant_start=-1.651182;Kurtosis_quant_stop=-1.761978;SVTYPE=INS;SUPTYPE=AL;SVLEN=11;STRANDS=+-;STRANDS2=31,21,31,21;RE=52;REF_strand=178972,173018;Strandbias_pval=0.214983;AF=0.000147731 GT:DR:DV 0/0:351938:52 +chr20 4687914 73 TTCTGGAAAAATCAACAACGCTCTTAGAT N . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4687935;STD_quant_start=2.097618;STD_quant_stop=3.044120;Kurtosis_quant_start=-0.490102;Kurtosis_quant_stop=-0.622138;SVTYPE=DEL;SUPTYPE=AL;SVLEN=-21;STRANDS=+-;STRANDS2=18,13,18,13;RE=31;REF_strand=178373,173000;Strandbias_pval=0.474728;AF=8.82253e-05 GT:DR:DV 0/0:351342:31 +chr20 4687912 74 N AAAAAAAAAAAAAAAAAAA . STRANDBIAS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4687912;STD_quant_start=0.500000;STD_quant_stop=6.112049;Kurtosis_quant_start=-0.171569;Kurtosis_quant_stop=-1.315550;SVTYPE=INS;SUPTYPE=AL;SVLEN=11;STRANDS=+-;STRANDS2=18,39,18,39;RE=57;REF_strand=178472,173006;Strandbias_pval=0.00494875;AF=0.000162172 GT:DR:DV 0/0:351421:57 +chr20 4687972 75 TTGTAGAAGAAAGGAAAAAATCACCAGTGGAAAGGAGCAATTTTACTTAC N . PASS IMPRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4687996;STD_quant_start=9.730486;STD_quant_stop=10.178409;Kurtosis_quant_start=-1.947120;Kurtosis_quant_stop=-1.835005;SVTYPE=DEL;SUPTYPE=AL;SVLEN=-24;STRANDS=+-;STRANDS2=90,81,90,81;RE=171;REF_strand=177519,172922;Strandbias_pval=0.646439;AF=0.000487957 GT:DR:DV 0/0:350270:171 +chr20 4687949 76 N AAAAAAAAAAAAAAAAAAAAAAAAAAA . STRANDBIAS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4687959;STD_quant_start=1.509231;STD_quant_stop=6.612278;Kurtosis_quant_start=-0.964806;Kurtosis_quant_stop=-0.754793;SVTYPE=INS;SUPTYPE=AL;SVLEN=13;STRANDS=+-;STRANDS2=9,27,9,27;RE=36;REF_strand=178031,172976;Strandbias_pval=0.00229475;AF=0.000102562 GT:DR:DV 0/0:350971:36 +chr20 4688011 77 N AAAAAAAAAAAAAAA . STRANDBIAS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4688011;STD_quant_start=0.000000;STD_quant_stop=1.842265;Kurtosis_quant_start=0.958620;Kurtosis_quant_stop=-0.646368;SVTYPE=INS;SUPTYPE=AL;SVLEN=11;STRANDS=+-;STRANDS2=12,54,12,54;RE=66;REF_strand=176718,172676;Strandbias_pval=8.14685e-08;AF=0.000188898 GT:DR:DV 0/0:349328:66 +chr20 28640980 78 N TTTCCTCTTTCTTTCTCT . PASS IMPRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=28641002;STD_quant_start=6.833740;STD_quant_stop=14.113823;Kurtosis_quant_start=-1.512029;Kurtosis_quant_stop=-1.863604;SVTYPE=INS;SUPTYPE=AL;SVLEN=18;STRANDS=+-;STRANDS2=11,3,11,3;RE=14;REF_strand=24,26;Strandbias_pval=0.067223;AF=0.28 GT:DR:DV 0/0:36:14 +chr20 28641074 79 N TTCTTTTTCTTTTCCCTTCTC . PASS IMPRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=28641077;STD_quant_start=4.989990;STD_quant_stop=17.088007;Kurtosis_quant_start=1.145751;Kurtosis_quant_stop=-1.276279;SVTYPE=INS;SUPTYPE=AL;SVLEN=48;STRANDS=+-;STRANDS2=6,6,6,6;RE=12;REF_strand=24,26;Strandbias_pval=1;AF=0.24 GT:DR:DV 0/0:38:12 +chr20 28641119 80 N CTTCCACTCCTTCT . PASS IMPRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=28641132;STD_quant_start=12.284136;STD_quant_stop=11.072488;Kurtosis_quant_start=-0.657425;Kurtosis_quant_stop=-1.541051;SVTYPE=INS;SUPTYPE=AL;SVLEN=14;STRANDS=+-;STRANDS2=10,3,10,3;RE=13;REF_strand=24,26;Strandbias_pval=0.11632;AF=0.26 GT:DR:DV 0/0:37:13 diff --git a/SVs_sniffles/vcf/47875_bodySnif.vcf b/SVs_sniffles/vcf/47875_bodySnif.vcf new file mode 100644 index 0000000..6e40530 --- /dev/null +++ b/SVs_sniffles/vcf/47875_bodySnif.vcf @@ -0,0 +1,38 @@ +##fileformat=VCFv4.1 +##source=Sniffles +##fileDate=20210810:54:43 AMef_minus +##contig= +##ALT= +##ALT= +##ALT= +##ALT= +##ALT= +##ALT= +##FILTER= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##FORMAT= +##FORMAT= +##FORMAT= +#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT bamfilt/47875_f.bam +chr20 4699401 0 N CATGGTGGCATGGGGCAGCCTCATGGTGGCTGGGGGCAGCCCCATGGTGGTGGCTGGGACAGCTTCCCCATGGTGGTGGCTGCGGCCCCATGGTGGTGGCTGGGGACAGCCTCATGGTGGTGGCTGGGGGCAGCCCCATGGTGGTGGCTGGGGACAGCCTCATGGTGGTGGCTGGGGGGCAGCCC . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4699402;STD_quant_start=7.332415;STD_quant_stop=7.211472;Kurtosis_quant_start=-1.606210;Kurtosis_quant_stop=-1.633301;SVTYPE=INS;SUPTYPE=AL;SVLEN=191;STRANDS=+-;STRANDS2=702,800,702,800;RE=1502;REF_strand=3982,4402;Strandbias_pval=0.59406;AF=0.179151 GT:DR:DV 0/0:6882:1502 +chr20 4699493 1 N GGGGCAGCCCCATGGTGGTGGCTGGGGACAGCCTCATGGTGGTGGCTGGGGGCAGCCCCATGGTGGTGGCTGGGGACAGCCTCATGGTGGTGGCTGGGGCAGCCCCACAGGCTGGGGGCAGCCTCATGGTGGTGGCTGGGGCAGCCCCATGGTGGCTGGGGACAGCCTCATGGTGGTGGCT . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4699493;STD_quant_start=8.296278;STD_quant_stop=3.899819;Kurtosis_quant_start=-1.931264;Kurtosis_quant_stop=-0.787690;SVTYPE=INS;SUPTYPE=AL;SVLEN=190;STRANDS=+-;STRANDS2=169,157,169,157;RE=326;REF_strand=3982,4402;Strandbias_pval=0.127238;AF=0.0388836 GT:DR:DV 0/0:8058:326 diff --git a/SVs_sniffles/vcf/47875_promoterSnif.vcf b/SVs_sniffles/vcf/47875_promoterSnif.vcf new file mode 100644 index 0000000..3b2dd5a --- /dev/null +++ b/SVs_sniffles/vcf/47875_promoterSnif.vcf @@ -0,0 +1,37 @@ +##fileformat=VCFv4.1 +##source=Sniffles +##fileDate=20210811:25:02 AMef_minus +##contig= +##ALT= +##ALT= +##ALT= +##ALT= +##ALT= +##ALT= +##FILTER= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##FORMAT= +##FORMAT= +##FORMAT= +#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT promoterbamfilt/47875_f.bam +chr20 4685224 0 TTTTTTTTTTT N . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4685236;STD_quant_start=0.000000;STD_quant_stop=0.836660;Kurtosis_quant_start=-0.153733;Kurtosis_quant_stop=0.761898;SVTYPE=DEL;SUPTYPE=AL;SVLEN=-12;STRANDS=+-;STRANDS2=12,8,12,8;RE=20;REF_strand=590,513;Strandbias_pval=0.654164;AF=0.0181324 GT:DR:DV 0/0:1083:20 diff --git a/SVs_sniffles/vcf/52331_bodySnif.vcf b/SVs_sniffles/vcf/52331_bodySnif.vcf new file mode 100644 index 0000000..9624e9c --- /dev/null +++ b/SVs_sniffles/vcf/52331_bodySnif.vcf @@ -0,0 +1,36 @@ +##fileformat=VCFv4.1 +##source=Sniffles +##fileDate=20210810:54:53 AMef_minus +##contig= +##ALT= +##ALT= +##ALT= +##ALT= +##ALT= +##ALT= +##FILTER= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##FORMAT= +##FORMAT= +##FORMAT= +#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT bamfilt/52331_f.bam diff --git a/SVs_sniffles/vcf/53689_bodySnif.vcf b/SVs_sniffles/vcf/53689_bodySnif.vcf new file mode 100644 index 0000000..1b8aa31 --- /dev/null +++ b/SVs_sniffles/vcf/53689_bodySnif.vcf @@ -0,0 +1,39 @@ +##fileformat=VCFv4.1 +##source=Sniffles +##fileDate=20210810:54:57 AMef_minus +##contig= +##ALT= +##ALT= +##ALT= +##ALT= +##ALT= +##ALT= +##FILTER= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##FORMAT= +##FORMAT= +##FORMAT= +#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT bamfilt/53689_f.bam +chr20 4699401 0 N CTGGTGGTGGCTGGGGGCAGCCTCATGGTGGTGGCTGGGGCAGCCCCATGGTGGTGGCTGGGGACAGCCTCATGGTGGTGGCTGGGGGCAGCCCCATGGTGGTGAGCGGGACAACCTCACGGTGGTGTGGGGGCAGCCCCATGGTGGTGGCTGGGGACAGCCTCATGGTGGTGGCTGGGGCAGCCC . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4699401;STD_quant_start=3.824170;STD_quant_stop=5.361139;Kurtosis_quant_start=-1.863002;Kurtosis_quant_stop=-1.003135;SVTYPE=INS;SUPTYPE=AL;SVLEN=190;STRANDS=+-;STRANDS2=513,526,513,526;RE=1039;REF_strand=4460,4514;Strandbias_pval=0.844205;AF=0.115779 GT:DR:DV 0/0:7935:1039 +chr20 4699439 1 N GGGGCAGCCCCATGGTGGTAATGGGGACAGCCTCATGGTGGTGGCTGGGGGCAGCCCCATGGTGGTGGCTGGGGACAGCCTCATGGTGGTGGCTGGGGGCAGCCCCCATGGTGGTGGCTGGGGACAGCCTCATGGTGGTGGCTGGGGGCAGCCCCATGGTGGTGGCTGGGGGCAGCCTCATGGTGGTGGCT . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4699439;STD_quant_start=5.147971;STD_quant_stop=6.354733;Kurtosis_quant_start=-1.722236;Kurtosis_quant_stop=-1.766515;SVTYPE=INS;SUPTYPE=AL;SVLEN=188;STRANDS=+-;STRANDS2=311,311,311,311;RE=622;REF_strand=4460,4514;Strandbias_pval=0.901039;AF=0.0693113 GT:DR:DV 0/0:8352:622 +chr20 4699493 2 N GCCCATGGTGGTGGCTGGGGACAGCCTCATGGTGGTGGCTGGGGGCAGCCCCATGGTGGTGGCTGGGGACAGCCTCATGGTGGTGGCTGGGGGCAGCCCATGGTGGTGGCTGGGGGCAGCCTCATGGTGGTGGCTGGGGCAGCCCCATGGTGGTGGCTGGGGACAGCCTCATGGCGGTGGCT . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4699493;STD_quant_start=6.451992;STD_quant_stop=6.164414;Kurtosis_quant_start=-1.609511;Kurtosis_quant_stop=-0.952916;SVTYPE=INS;SUPTYPE=AL;SVLEN=193;STRANDS=+-;STRANDS2=164,149,164,149;RE=313;REF_strand=4460,4514;Strandbias_pval=0.357952;AF=0.0348785 GT:DR:DV 0/0:8661:313 diff --git a/SVs_sniffles/vcf/53689_promoterSnif.vcf b/SVs_sniffles/vcf/53689_promoterSnif.vcf new file mode 100644 index 0000000..062989d --- /dev/null +++ b/SVs_sniffles/vcf/53689_promoterSnif.vcf @@ -0,0 +1,38 @@ +##fileformat=VCFv4.1 +##source=Sniffles +##fileDate=20210811:25:02 AMef_minus +##contig= +##ALT= +##ALT= +##ALT= +##ALT= +##ALT= +##ALT= +##FILTER= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##FORMAT= +##FORMAT= +##FORMAT= +#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT promoterbamfilt/53689_f.bam +chr20 4685224 0 TTTTTTTTTTT N . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4685235;STD_quant_start=0.000000;STD_quant_stop=1.643168;Kurtosis_quant_start=2.893536;Kurtosis_quant_stop=-0.672287;SVTYPE=DEL;SUPTYPE=AL,NR;SVLEN=-11;STRANDS=+-;STRANDS2=12,3,12,3;RE=15;REF_strand=821,133;Strandbias_pval=0.455086;AF=0.0157233 GT:DR:DV 0/0:939:15 +chr20 4685224 1 N TTTTTTTTTTTTT . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4685226;STD_quant_start=0.000000;STD_quant_stop=1.549193;Kurtosis_quant_start=nan;Kurtosis_quant_stop=-0.083333;SVTYPE=INS;SUPTYPE=AL;SVLEN=11;STRANDS=+-;STRANDS2=12,0,12,0;RE=12;REF_strand=820,132;Strandbias_pval=0.388266;AF=0.012605 GT:DR:DV 0/0:940:12 diff --git a/SVs_sniffles/vcf/53747_bodySnif.vcf b/SVs_sniffles/vcf/53747_bodySnif.vcf new file mode 100644 index 0000000..5934659 --- /dev/null +++ b/SVs_sniffles/vcf/53747_bodySnif.vcf @@ -0,0 +1,40 @@ +##fileformat=VCFv4.1 +##source=Sniffles +##fileDate=20210810:55:07 AMef_minus +##contig= +##ALT= +##ALT= +##ALT= +##ALT= +##ALT= +##ALT= +##FILTER= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##FORMAT= +##FORMAT= +##FORMAT= +#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT bamfilt/53747_f.bam +chr20 4699380 0 N GGTGGTGGCTGGGGGCAGCCTCATGGTAGTACTGGGCAGCCTCATGGTGGTGGCCGGGGGCAGCCTCATGGTGGTGGCTGGGGGCAGCCCCCATGGTGGTGGCTGGGGAATAGCCATGGTGGTGGCTGGGGGGGCAGCCCCAT . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4699381;STD_quant_start=3.645298;STD_quant_stop=4.159849;Kurtosis_quant_start=-1.564282;Kurtosis_quant_stop=-1.493821;SVTYPE=INS;SUPTYPE=AL;SVLEN=143;STRANDS=+-;STRANDS2=755,856,755,856;RE=1611;REF_strand=6070,6882;Strandbias_pval=1;AF=0.124382 GT:DR:DV 0/0:11341:1611 +chr20 4699380 1 N GGTGGTGGCTGGGGGCAGCCTCAT . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4699380;STD_quant_start=2.556702;STD_quant_stop=4.588120;Kurtosis_quant_start=-1.366580;Kurtosis_quant_stop=-1.170816;SVTYPE=INS;SUPTYPE=AL;SVLEN=23;STRANDS=+-;STRANDS2=146,208,146,208;RE=354;REF_strand=6070,6882;Strandbias_pval=0.0400867;AF=0.0273317 GT:DR:DV 0/0:12598:354 +chr20 4699439 2 N GGGGCAGCCTCATGGTGGTGGCTGGGGGCAGCCCCATGGTGGTGGCTGGGGACAGCCTCATGGTGGTGTGGGGGCAGCCCCATGGTGGTGGCTGGGGGCAGCCTCGGTGGTGGCTGGGGGCAGCCTCATGGTGGTGGCT . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4699441;STD_quant_start=1.110750;STD_quant_stop=3.497680;Kurtosis_quant_start=2.291462;Kurtosis_quant_stop=-0.446804;SVTYPE=INS;SUPTYPE=AL;SVLEN=142;STRANDS=+-;STRANDS2=308,309,308,309;RE=617;REF_strand=6070,6882;Strandbias_pval=0.148455;AF=0.0476374 GT:DR:DV 0/0:12335:617 +chr20 4699463 3 N GCCGGGGGCAGCCCCATGGTGGTGGCTGGGGACAGCCTCATGGTGGTGGCTGGGGCAGCCCCATGGTGGTGGCTGGGGGCAGCCTCATGGTGGTGGCTGGGGCAGCCTCATGGTGGTGGCTGGGGCAGCCCCATGGTGGGTGGT . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4699485;STD_quant_start=6.119087;STD_quant_stop=4.087415;Kurtosis_quant_start=-0.879644;Kurtosis_quant_stop=-1.387914;SVTYPE=INS;SUPTYPE=AL;SVLEN=118;STRANDS=+-;STRANDS2=257,290,257,290;RE=547;REF_strand=6070,6882;Strandbias_pval=0.965136;AF=0.0422329 GT:DR:DV 0/0:12405:547 diff --git a/SVs_sniffles/vcf/53747_promoterSnif.vcf b/SVs_sniffles/vcf/53747_promoterSnif.vcf new file mode 100644 index 0000000..e1edb9f --- /dev/null +++ b/SVs_sniffles/vcf/53747_promoterSnif.vcf @@ -0,0 +1,37 @@ +##fileformat=VCFv4.1 +##source=Sniffles +##fileDate=20210811:25:02 AMef_minus +##contig= +##ALT= +##ALT= +##ALT= +##ALT= +##ALT= +##ALT= +##FILTER= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##FORMAT= +##FORMAT= +##FORMAT= +#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT promoterbamfilt/53747_f.bam +chr20 4685224 0 TTTTTTTTTTTTT N . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4685237;STD_quant_start=1.133893;STD_quant_stop=2.070197;Kurtosis_quant_start=1.252544;Kurtosis_quant_stop=0.938199;SVTYPE=DEL;SUPTYPE=AL;SVLEN=-13;STRANDS=+-;STRANDS2=19,9,19,9;RE=28;REF_strand=570,681;Strandbias_pval=0.0215392;AF=0.0223821 GT:DR:DV 0/0:1223:28 diff --git a/SVs_sniffles/vcf/54493_bodySnif.vcf b/SVs_sniffles/vcf/54493_bodySnif.vcf new file mode 100644 index 0000000..4fe2065 --- /dev/null +++ b/SVs_sniffles/vcf/54493_bodySnif.vcf @@ -0,0 +1,38 @@ +##fileformat=VCFv4.1 +##source=Sniffles +##fileDate=20210810:55:27 AMef_minus +##contig= +##ALT= +##ALT= +##ALT= +##ALT= +##ALT= +##ALT= +##FILTER= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##FORMAT= +##FORMAT= +##FORMAT= +#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT bamfilt/54493_f.bam +chr20 4690845 0 N AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA . PASS IMPRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4690845;STD_quant_start=16.337074;STD_quant_stop=12.401613;Kurtosis_quant_start=-1.461001;Kurtosis_quant_stop=0.380189;SVTYPE=INS;SUPTYPE=AL;SVLEN=65;STRANDS=+-;STRANDS2=3,9,3,9;RE=12;REF_strand=12126,12750;Strandbias_pval=0.147447;AF=0.000482393 GT:DR:DV 0/0:24864:12 +chr20 4694354 1 N AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA . PASS IMPRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4694354;STD_quant_start=16.015617;STD_quant_stop=20.359273;Kurtosis_quant_start=0.004434;Kurtosis_quant_stop=-0.437333;SVTYPE=INS;SUPTYPE=AL;SVLEN=51;STRANDS=+-;STRANDS2=3,5,3,5;RE=8;REF_strand=12128,12750;Strandbias_pval=0.727206;AF=0.000321569 GT:DR:DV 0/0:24870:8 diff --git a/SVs_sniffles/vcf/54493_promoterSnif.vcf b/SVs_sniffles/vcf/54493_promoterSnif.vcf new file mode 100644 index 0000000..4a58d7d --- /dev/null +++ b/SVs_sniffles/vcf/54493_promoterSnif.vcf @@ -0,0 +1,61 @@ +##fileformat=VCFv4.1 +##source=Sniffles +##fileDate=20210811:25:03 AMef_minus +##contig= +##ALT= +##ALT= +##ALT= +##ALT= +##ALT= +##ALT= +##FILTER= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##FORMAT= +##FORMAT= +##FORMAT= +#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT promoterbamfilt/54493_f.bam +chr20 4685224 0 N TTTTTTTTTTT . STRANDBIAS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4685224;STD_quant_start=0.000000;STD_quant_stop=1.242368;Kurtosis_quant_start=29.774441;Kurtosis_quant_stop=1.629936;SVTYPE=INS;SUPTYPE=AL;SVLEN=11;STRANDS=+-;STRANDS2=362,7,362,7;RE=369;REF_strand=13518,7366;Strandbias_pval=4.75532e-57;AF=0.017669 GT:DR:DV 0/0:20515:369 +chr20 4685224 1 TTTTTTTTTTTTTT N . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4685235;STD_quant_start=0.000000;STD_quant_stop=1.107436;Kurtosis_quant_start=3.861587;Kurtosis_quant_stop=3.047001;SVTYPE=DEL;SUPTYPE=AL;SVLEN=-11;STRANDS=+-;STRANDS2=63,43,63,43;RE=106;REF_strand=13518,7368;Strandbias_pval=0.263311;AF=0.00507517 GT:DR:DV 0/0:20780:106 +chr20 4685324 2 GCAGCCTCTACC N . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4685342;STD_quant_start=4.732864;STD_quant_stop=6.723095;Kurtosis_quant_start=-1.709466;Kurtosis_quant_stop=-1.807353;SVTYPE=DEL;SUPTYPE=AL;SVLEN=-18;STRANDS=+-;STRANDS2=15,6,15,6;RE=21;REF_strand=13520,7390;Strandbias_pval=0.6501;AF=0.0010043 GT:DR:DV 0/0:20889:21 +chr20 4685413 3 N TTTTTTTTTTTTTTTTT . STRANDBIAS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4685418;STD_quant_start=0.000000;STD_quant_stop=3.251373;Kurtosis_quant_start=0.134424;Kurtosis_quant_stop=-0.273725;SVTYPE=INS;SUPTYPE=AL;SVLEN=12;STRANDS=+-;STRANDS2=26,2,26,2;RE=28;REF_strand=13522,7417;Strandbias_pval=0.00110117;AF=0.00133722 GT:DR:DV 0/0:20911:28 +chr20 4685624 4 ATTTTCCCCAGGGCATGCCTGGTTTA N . PASS IMPRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4685658;STD_quant_start=17.222079;STD_quant_stop=15.079788;Kurtosis_quant_start=-0.249322;Kurtosis_quant_stop=-1.300195;SVTYPE=DEL;SUPTYPE=AL;SVLEN=-34;STRANDS=+-;STRANDS2=8,2,8,2;RE=10;REF_strand=13522,7505;Strandbias_pval=0.510674;AF=0.000475579 GT:DR:DV 0/0:21017:10 +chr20 4685777 5 CGCAAGAACACAC N . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4685790;STD_quant_start=2.254625;STD_quant_stop=2.986079;Kurtosis_quant_start=-1.490542;Kurtosis_quant_stop=-1.296637;SVTYPE=DEL;SUPTYPE=AL;SVLEN=-13;STRANDS=+-;STRANDS2=21,3,21,3;RE=24;REF_strand=13522,7553;Strandbias_pval=0.0177555;AF=0.00113879 GT:DR:DV 0/0:21051:24 +chr20 4686076 6 TTCCTGAGCCT N . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4686091;STD_quant_start=2.276361;STD_quant_stop=2.522625;Kurtosis_quant_start=-1.553877;Kurtosis_quant_stop=-1.603865;SVTYPE=DEL;SUPTYPE=AL;SVLEN=-15;STRANDS=+-;STRANDS2=20,3,20,3;RE=23;REF_strand=12972,7670;Strandbias_pval=0.0165793;AF=0.00111423 GT:DR:DV 0/0:20619:23 +chr20 4686326 7 GGGGGCACAGAGTGTGCGCCGGGCCGCGCGGCAATTGGTCCCCGCGCCGACCTCCGCCCGCGAGCGCCGCCGCTTCCCTTCCCCGCCCCGCGTCCCTCCCCCTCGGCCCCGCGCGTCGCCTGTCCTCCGAGCCAGTCGCTGACAGCCGCGGCGCCGCGAGCTTCTCCTCTCCTCACGACCGAGGCAGGTAAACGCCCGGGGTGGGAGGAACGCGGGCGGGGGCAGGGGAGCCGCGGGGGCCGAGTGAGGACCCCGGGCCTCGGGTCCCAGGCGCAAGGGTGCCCGGCCGGGCGGGGTCGGGACCCCAGTGAGGAGGGGCCGGGGGCTGCCCCGCGGGCGCGTGACGCGTCTCGGGCCTGCCCGGCTGCGCTGGTCTCCGCTCGGGTGAGGCGGCTTGGCTTCGCTTTTCAGGTTAGGAAAGCTCCCTTTACTGCGCGTTGGGGGGCTGGGGGAGCTGGCGGAGCCCCGTTAGGGAGGTCGGTGGCGCCGGGGTGTCTCAGCGCCCCCTGCACCCCGCGCGGGTCCGGCCCAGCGGGCGATCGCTGGCGCCCAGGGAACTCCGGGAGGGCCGCCAGCGGGCTCCGCAGGGCGCGGGGCGGGGAGGGGCGCCTGGGGGCCGCGGGGCTCGCGCTCCCCGCCCGTTGGCCGCCCCTCGGAGGCCGAGATCGGGGCCCAGAACGCCCCTTGGCAAGGCCTGGCGCTTCCGCGATGCCCAGAGGGTGCTTGGGGGGATGGAGAGAGGGGCGCCCGCCG N . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4687079;STD_quant_start=0.000000;STD_quant_stop=0.115470;Kurtosis_quant_start=-0.116407;Kurtosis_quant_stop=2.443291;SVTYPE=DEL;SUPTYPE=AL,SR;SVLEN=-753;STRANDS=+-;STRANDS2=94,56,94,56;RE=150;REF_strand=10786,8051;Strandbias_pval=0.186109;AF=0.00796305 GT:DR:DV 0/0:18687:150 +chr20 4686486 8 CTTCTCCTCTCC N . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4686497;STD_quant_start=2.720294;STD_quant_stop=2.121320;Kurtosis_quant_start=-1.126375;Kurtosis_quant_stop=-1.051421;SVTYPE=DEL;SUPTYPE=AL;SVLEN=-11;STRANDS=+-;STRANDS2=11,9,11,9;RE=20;REF_strand=10730,7859;Strandbias_pval=0.824014;AF=0.00107591 GT:DR:DV 0/0:18569:20 +chr20 4686546 9 GGGGAGCCGCG N . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4686560;STD_quant_start=6.833740;STD_quant_stop=6.985700;Kurtosis_quant_start=-1.398858;Kurtosis_quant_stop=-1.464842;SVTYPE=DEL;SUPTYPE=AL;SVLEN=-14;STRANDS=+-;STRANDS2=9,8,9,8;RE=17;REF_strand=10573,7880;Strandbias_pval=0.807877;AF=0.000921259 GT:DR:DV 0/0:18436:17 +chr20 4686578 10 CCGGGCCTCGG N . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4686591;STD_quant_start=6.715653;STD_quant_stop=6.131884;Kurtosis_quant_start=-1.308495;Kurtosis_quant_stop=-0.193773;SVTYPE=DEL;SUPTYPE=AL;SVLEN=-13;STRANDS=+-;STRANDS2=13,3,13,3;RE=16;REF_strand=10534,7889;Strandbias_pval=0.0741798;AF=0.00086848 GT:DR:DV 0/0:18407:16 +chr20 4686641 11 GGGGCCGGGGGCTGCCCCGC N . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4686660;STD_quant_start=8.043153;STD_quant_stop=8.757414;Kurtosis_quant_start=-1.296099;Kurtosis_quant_stop=-1.370433;SVTYPE=DEL;SUPTYPE=AL;SVLEN=-19;STRANDS=+-;STRANDS2=10,16,10,16;RE=26;REF_strand=10502,7912;Strandbias_pval=0.0730388;AF=0.00141197 GT:DR:DV 0/0:18388:26 +chr20 4686933 12 GGGGGCCGCGGGGCTC N . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4686951;STD_quant_start=6.801703;STD_quant_stop=8.491482;Kurtosis_quant_start=-0.725605;Kurtosis_quant_stop=-1.176961;SVTYPE=DEL;SUPTYPE=AL;SVLEN=-18;STRANDS=+-;STRANDS2=19,19,19,19;RE=38;REF_strand=10248,8097;Strandbias_pval=0.514721;AF=0.00207141 GT:DR:DV 0/0:18307:38 +chr20 4687155 13 TCGCCGCCTGAGCTTCTCCGAG N . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4687177;STD_quant_start=6.685806;STD_quant_stop=8.449852;Kurtosis_quant_start=-1.151367;Kurtosis_quant_stop=0.101203;SVTYPE=DEL;SUPTYPE=AL;SVLEN=-22;STRANDS=+-;STRANDS2=7,7,7,7;RE=14;REF_strand=10122,8432;Strandbias_pval=0.792376;AF=0.000754554 GT:DR:DV 0/0:18540:14 +chr20 4687590 14 N TTTTTTTGCAC . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4687593;STD_quant_start=6.371813;STD_quant_stop=8.608136;Kurtosis_quant_start=0.028496;Kurtosis_quant_stop=-0.405193;SVTYPE=INS;SUPTYPE=AL;SVLEN=18;STRANDS=+-;STRANDS2=10,1,10,1;RE=11;REF_strand=9891,8432;Strandbias_pval=0.0145006;AF=0.000600338 GT:DR:DV 0/0:18312:11 +chr20 25865949 15 N GCAGCGAGGCTCCTGCTGCAGCCGAGGCGGCA . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=25865949;STD_quant_start=0.000000;STD_quant_stop=0.522233;Kurtosis_quant_start=-1.041820;Kurtosis_quant_stop=-0.958100;SVTYPE=INS;SUPTYPE=AL;SVLEN=32;STRANDS=+-;STRANDS2=11,12,11,12;RE=23;REF_strand=34,24;Strandbias_pval=0.459681;AF=0.396552 GT:DR:DV 0/1:35:23 +chr20 25866706 16 N CCCAGCGCCAG . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=25866706;STD_quant_start=0.000000;STD_quant_stop=0.000000;Kurtosis_quant_start=7.000000;Kurtosis_quant_stop=7.000000;SVTYPE=INS;SUPTYPE=AL;SVLEN=11;STRANDS=+-;STRANDS2=5,8,5,8;RE=13;REF_strand=34,24;Strandbias_pval=0.22675;AF=0.224138 GT:DR:DV 0/0:45:13 +chr20 25867788 17 N CCCAGACACACACAGACACACACACAGACACACACC . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=25867788;STD_quant_start=0.000000;STD_quant_stop=0.377964;Kurtosis_quant_start=-0.210586;Kurtosis_quant_stop=3.439280;SVTYPE=INS;SUPTYPE=AL;SVLEN=36;STRANDS=+-;STRANDS2=16,12,16,12;RE=28;REF_strand=32,24;Strandbias_pval=1;AF=0.5 GT:DR:DV 0/1:28:28 +chr20 28640917 18 N TTTCTTTCTCTTCTTTCTTTCTTTCTTTCTTT . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=28640938;STD_quant_start=3.510853;STD_quant_stop=8.027128;Kurtosis_quant_start=-1.869586;Kurtosis_quant_stop=-1.853308;SVTYPE=INS;SUPTYPE=AL;SVLEN=11;STRANDS=+-;STRANDS2=29,63,29,63;RE=92;REF_strand=220,484;Strandbias_pval=1;AF=0.130682 GT:DR:DV 0/0:612:92 +chr20 28640975 19 N CTTTCTTTCTTCTGTTTCTCTCTCTCTCCTTCTTTCA . STRANDBIAS IMPRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=28640999;STD_quant_start=11.060871;STD_quant_stop=12.993955;Kurtosis_quant_start=-1.837328;Kurtosis_quant_stop=-2.099939;SVTYPE=INS;SUPTYPE=AL;SVLEN=12;STRANDS=+-;STRANDS2=60,80,60,80;RE=140;REF_strand=220,487;Strandbias_pval=0.00796623;AF=0.19802 GT:DR:DV 0/0:567:140 +chr20 28641006 20 N TTCTTTCTTTCTTCTCTCTTTCTCTTTCTTTCTCTCTCTTTCTTTT . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=28641006;STD_quant_start=0.000000;STD_quant_stop=1.369306;Kurtosis_quant_start=0.320739;Kurtosis_quant_stop=0.051573;SVTYPE=INS;SUPTYPE=AL;SVLEN=45;STRANDS=+-;STRANDS2=22,27,22,27;RE=49;REF_strand=220,488;Strandbias_pval=0.0564901;AF=0.069209 GT:DR:DV 0/0:659:49 +chr20 28641074 21 N TTCCTTTCCTCTTCTCCTTTCCTTTCTCTTTCCTTTTCTTTTTTCTTTTTCCCTTTCTC . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=28641110;STD_quant_start=4.729527;STD_quant_stop=7.906249;Kurtosis_quant_start=-1.455325;Kurtosis_quant_stop=-1.698763;SVTYPE=INS;SUPTYPE=AL;SVLEN=15;STRANDS=+-;STRANDS2=36,79,36,79;RE=115;REF_strand=219,492;Strandbias_pval=0.91367;AF=0.161744 GT:DR:DV 0/0:596:115 +chr20 28641119 22 N CCTTCCTTTCCTTCCTTCCTTCCTTCCT . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=28641119;STD_quant_start=0.000000;STD_quant_stop=1.109400;Kurtosis_quant_start=-0.577814;Kurtosis_quant_stop=0.185806;SVTYPE=INS;SUPTYPE=AL;SVLEN=27;STRANDS=+-;STRANDS2=12,15,12,15;RE=27;REF_strand=218,492;Strandbias_pval=0.141244;AF=0.0380282 GT:DR:DV 0/0:683:27 +chr20 28641148 23 N CTTCCTTCCTTCCTTCCTTCCTTTCTTCCT . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=28641148;STD_quant_start=2.743977;STD_quant_stop=2.985258;Kurtosis_quant_start=-0.962698;Kurtosis_quant_stop=-0.678686;SVTYPE=INS;SUPTYPE=AL;SVLEN=36;STRANDS=+-;STRANDS2=20,48,20,48;RE=68;REF_strand=218,492;Strandbias_pval=0.891018;AF=0.0957746 GT:DR:DV 0/0:642:68 +chr20 29438337 24 TGAAGTCACAGCCTCACAGTTATGTTGAATCTTGGTCTGAGAGTCACCAACCCATGAGTATCCATATATAAGTCAATTTTTCCCACCTTTGACTGACTACAGGTGTGAGATTCAGAACCTCAACAG N . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=29438463;STD_quant_start=1.702939;STD_quant_stop=2.024846;Kurtosis_quant_start=4.479191;Kurtosis_quant_stop=1.098751;SVTYPE=DEL;SUPTYPE=AL;SVLEN=-126;STRANDS=+-;STRANDS2=5,5,5,5;RE=10;REF_strand=10,12;Strandbias_pval=1;AF=0.454545 GT:DR:DV 0/1:12:10 diff --git a/SVs_sniffles/vcf/54890_bodySnif.vcf b/SVs_sniffles/vcf/54890_bodySnif.vcf new file mode 100644 index 0000000..1f72a61 --- /dev/null +++ b/SVs_sniffles/vcf/54890_bodySnif.vcf @@ -0,0 +1,36 @@ +##fileformat=VCFv4.1 +##source=Sniffles +##fileDate=20210810:55:38 AMef_minus +##contig= +##ALT= +##ALT= +##ALT= +##ALT= +##ALT= +##ALT= +##FILTER= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##FORMAT= +##FORMAT= +##FORMAT= +#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT bamfilt/54890_f.bam diff --git a/SVs_sniffles/vcf/54890_promoterSnif.vcf b/SVs_sniffles/vcf/54890_promoterSnif.vcf new file mode 100644 index 0000000..69f76cb --- /dev/null +++ b/SVs_sniffles/vcf/54890_promoterSnif.vcf @@ -0,0 +1,56 @@ +##fileformat=VCFv4.1 +##source=Sniffles +##fileDate=20210811:25:06 AMef_minus +##contig= +##ALT= +##ALT= +##ALT= +##ALT= +##ALT= +##ALT= +##FILTER= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##FORMAT= +##FORMAT= +##FORMAT= +#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT promoterbamfilt/54890_f.bam +chr20 4685105 0 CATTCTCCTGGCTTCTCC N . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4685122;STD_quant_start=4.289522;STD_quant_stop=5.412947;Kurtosis_quant_start=-1.019736;Kurtosis_quant_stop=-1.094253;SVTYPE=DEL;SUPTYPE=AL;SVLEN=-17;STRANDS=+-;STRANDS2=13,2,13,2;RE=15;REF_strand=18326,3569;Strandbias_pval=1;AF=0.000685088 GT:DR:DV 0/0:21880:15 +chr20 4685224 1 TTTTTTTTTTT N . STRANDBIAS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4685235;STD_quant_start=0.272166;STD_quant_stop=1.433721;Kurtosis_quant_start=0.282939;Kurtosis_quant_stop=0.035096;SVTYPE=DEL;SUPTYPE=AL,NR;SVLEN=-11;STRANDS=+-;STRANDS2=76,32,76,32;RE=108;REF_strand=18346,3626;Strandbias_pval=0.000644664;AF=0.00491535 GT:DR:DV 0/0:21864:108 +chr20 4685224 2 N TTTTTTTTTTTTTTTTT . STRANDBIAS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4685224;STD_quant_start=0.000000;STD_quant_stop=1.173273;Kurtosis_quant_start=118.182024;Kurtosis_quant_stop=0.432347;SVTYPE=INS;SUPTYPE=AL;SVLEN=11;STRANDS=+-;STRANDS2=478,1,478,1;RE=479;REF_strand=18346,3622;Strandbias_pval=1.6746e-35;AF=0.0218044 GT:DR:DV 0/0:21489:479 +chr20 4685335 3 TCCTGGGCTCAAGCAA N . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4685353;STD_quant_start=7.720104;STD_quant_stop=7.106335;Kurtosis_quant_start=-1.615714;Kurtosis_quant_stop=-1.840625;SVTYPE=DEL;SUPTYPE=AL;SVLEN=-18;STRANDS=+-;STRANDS2=16,4,16,4;RE=20;REF_strand=18364,3654;Strandbias_pval=0.761636;AF=0.000908348 GT:DR:DV 0/0:21998:20 +chr20 4685413 4 N TTTTTTTATTTTTTTTT . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4685418;STD_quant_start=0.000000;STD_quant_stop=4.330127;Kurtosis_quant_start=0.106287;Kurtosis_quant_stop=-1.121079;SVTYPE=INS;SUPTYPE=AL;SVLEN=12;STRANDS=+-;STRANDS2=22,3,22,3;RE=25;REF_strand=18364,3666;Strandbias_pval=0.787639;AF=0.00113482 GT:DR:DV 0/0:22005:25 +chr20 4685636 5 ATGCCTGGTTTACGCCCATTTCACTTT N . PASS IMPRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4685658;STD_quant_start=10.108502;STD_quant_stop=10.689842;Kurtosis_quant_start=-2.134898;Kurtosis_quant_stop=-2.081137;SVTYPE=DEL;SUPTYPE=AL,NR;SVLEN=-22;STRANDS=+-;STRANDS2=19,4,19,4;RE=23;REF_strand=18364,3689;Strandbias_pval=1;AF=0.00104294 GT:DR:DV 0/0:22030:23 +chr20 4685922 6 AAGGAACAGGTGA N . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4685941;STD_quant_start=9.974969;STD_quant_stop=9.027735;Kurtosis_quant_start=-1.779021;Kurtosis_quant_stop=-1.955366;SVTYPE=DEL;SUPTYPE=AL;SVLEN=-19;STRANDS=+-;STRANDS2=20,1,20,1;RE=21;REF_strand=18359,3744;Strandbias_pval=0.237831;AF=0.000950097 GT:DR:DV 0/0:22082:21 +chr20 4686077 7 CATTCCTGAGC N . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4686089;STD_quant_start=2.420153;STD_quant_stop=3.070598;Kurtosis_quant_start=-1.532909;Kurtosis_quant_stop=-1.661156;SVTYPE=DEL;SUPTYPE=AL;SVLEN=-12;STRANDS=+-;STRANDS2=26,3,26,3;RE=29;REF_strand=17914,3781;Strandbias_pval=0.461689;AF=0.00133671 GT:DR:DV 0/0:21666:29 +chr20 4686285 8 GCTGCACCCTTTAACTT N . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4686302;STD_quant_start=5.449771;STD_quant_stop=9.433981;Kurtosis_quant_start=-1.207131;Kurtosis_quant_stop=-1.518644;SVTYPE=DEL;SUPTYPE=AL;SVLEN=-17;STRANDS=+-;STRANDS2=16,0,16,0;RE=16;REF_strand=16888,3808;Strandbias_pval=0.0558011;AF=0.000773096 GT:DR:DV 0/0:20680:16 +chr20 4686326 9 GGGGGCACAGAGTGTGCGCCGGGCCGCGCGGCAATTGGTCCCCGCGCCGACCTCCGCCCGCGAGCGCCGCCGCTTCCCTTCCCCGCCCCGCGTCCCTCCCCCTCGGCCCCGCGCGTCGCCTGTCCTCCGAGCCAGTCGCTGACAGCCGCGGCGCCGCGAGCTTCTCCTCTCCTCACGACCGAGGCAGGTAAACGCCCGGGGTGGGAGGAACGCGGGCGGGGGCAGGGGAGCCGCGGGGGCCGAGTGAGGACCCCGGGCCTCGGGTCCCAGGCGCAAGGGTGCCCGGCCGGGCGGGGTCGGGACCCCAGTGAGGAGGGGCCGGGGGCTGCCCCGCGGGCGCGTGACGCGTCTCGGGCCTGCCCGGCTGCGCTGGTCTCCGCTCGGGTGAGGCGGCTTGGCTTCGCTTTTCAGGTTAGGAAAGCTCCCTTTACTGCGCGTTGGGGGGCTGGGGGAGCTGGCGGAGCCCCGTTAGGGAGGTCGGTGGCGCCGGGGTGTCTCAGCGCCCCCTGCACCCCGCGCGGGTCCGGCCCAGCGGGCGATCGCTGGCGCCCAGGGAACTCCGGGAGGGCCGCCAGCGGGCTCCGCAGGGCGCGGGGCGGGGAGGGGCGCCTGGGGGCCGCGGGGCTCGCGCTCCCCGCCCGTTGGCCGCCCCTCGGAGGCCGAGATCGGGGCCCAGAACGCCCCTTGGCAAGGCCTGGCGCTTCCGCGATGCCCAGAGGGTGCTTGGGGGGATGGAGAGAGGGGCGCCCGCCG N . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4687079;STD_quant_start=0.258199;STD_quant_stop=0.632456;Kurtosis_quant_start=-0.133747;Kurtosis_quant_stop=1.961346;SVTYPE=DEL;SUPTYPE=AL;SVLEN=-753;STRANDS=+-;STRANDS2=72,19,72,19;RE=91;REF_strand=15964,3917;Strandbias_pval=0.791562;AF=0.00457723 GT:DR:DV 0/0:19790:91 +chr20 4686402 10 CCTTCCCCGCCCCG N . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4686416;STD_quant_start=6.244998;STD_quant_stop=5.735852;Kurtosis_quant_start=-1.359155;Kurtosis_quant_stop=-1.448161;SVTYPE=DEL;SUPTYPE=AL;SVLEN=-14;STRANDS=+-;STRANDS2=13,4,13,4;RE=17;REF_strand=16311,3831;Strandbias_pval=0.548157;AF=0.000844008 GT:DR:DV 0/0:20125:17 +chr20 4686485 11 GCTTCTCCTCT N . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4686497;STD_quant_start=2.801099;STD_quant_stop=3.281651;Kurtosis_quant_start=-1.259969;Kurtosis_quant_stop=-1.212943;SVTYPE=DEL;SUPTYPE=AL;SVLEN=-12;STRANDS=+-;STRANDS2=21,5,21,5;RE=26;REF_strand=16013,3845;Strandbias_pval=1;AF=0.0013093 GT:DR:DV 0/0:19832:26 +chr20 4686550 12 GGCAGGGGAGCCGCGGGGGCCGAGT N . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4686569;STD_quant_start=6.300183;STD_quant_stop=4.930283;Kurtosis_quant_start=-1.466767;Kurtosis_quant_stop=-0.984135;SVTYPE=DEL;SUPTYPE=AL;SVLEN=-19;STRANDS=+-;STRANDS2=22,4,22,4;RE=26;REF_strand=15843,3857;Strandbias_pval=0.80497;AF=0.0013198 GT:DR:DV 0/0:19674:26 +chr20 4686577 13 CCCAGGCGCAAGGGTGC N . PASS IMPRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4686602;STD_quant_start=9.731393;STD_quant_stop=12.980755;Kurtosis_quant_start=-0.311769;Kurtosis_quant_stop=0.177570;SVTYPE=DEL;SUPTYPE=AL;SVLEN=-25;STRANDS=+-;STRANDS2=8,3,8,3;RE=11;REF_strand=15807,3863;Strandbias_pval=0.460894;AF=0.000559227 GT:DR:DV 0/0:19659:11 +chr20 4686996 14 CCCAGAACGCC N . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4687009;STD_quant_start=4.254409;STD_quant_stop=4.939636;Kurtosis_quant_start=2.413177;Kurtosis_quant_stop=1.904659;SVTYPE=DEL;SUPTYPE=AL;SVLEN=-13;STRANDS=+-;STRANDS2=14,0,14,0;RE=14;REF_strand=15318,3981;Strandbias_pval=0.0894387;AF=0.000725426 GT:DR:DV 0/0:19285:14 +chr20 4687275 15 GTCCGGGGAGGCCCCA N . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4687289;STD_quant_start=5.707797;STD_quant_stop=5.712406;Kurtosis_quant_start=-1.418827;Kurtosis_quant_stop=-1.368105;SVTYPE=DEL;SUPTYPE=AL;SVLEN=-14;STRANDS=+-;STRANDS2=27,12,27,12;RE=39;REF_strand=15120,4050;Strandbias_pval=0.166827;AF=0.00203443 GT:DR:DV 0/0:19131:39 +chr20 11733671 16 N TTGTATGGCAAAGGACACAAACAGATACCTCAAAAGAAGATATGCAAGCAGCCAAAAATAATATGAGAAAAGATGCTCAGAATCTCTAAGGAGATTAGAGAAATGCAAATCAAAACCACAATGAAATATTATCTCATACCAGTCAGTA . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=11733671;STD_quant_start=0.000000;STD_quant_stop=1.328422;Kurtosis_quant_start=-1.015127;Kurtosis_quant_stop=-0.604761;SVTYPE=INS;SUPTYPE=AL;SVLEN=147;STRANDS=+-;STRANDS2=31,4,31,4;RE=35;REF_strand=66,10;Strandbias_pval=1;AF=0.460526 GT:DR:DV 0/1:41:35 +chr20 29408716 17 N CTTCCGTTTCTCATCTT . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=29408716;STD_quant_start=0.000000;STD_quant_stop=1.015038;Kurtosis_quant_start=5.651267;Kurtosis_quant_stop=4.624591;SVTYPE=INS;SUPTYPE=AL;SVLEN=18;STRANDS=+-;STRANDS2=31,35,31,35;RE=66;REF_strand=116,140;Strandbias_pval=0.889921;AF=0.257812 GT:DR:DV 0/0:190:66 +chr20 29409484 18 GGGCCGCTGAGCGCCCCGCTGGCCAAAGGGGCTGT N . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=29409519;STD_quant_start=0.000000;STD_quant_stop=0.000000;Kurtosis_quant_start=2.050488;Kurtosis_quant_stop=1.465342;SVTYPE=DEL;SUPTYPE=AL;SVLEN=-35;STRANDS=+-;STRANDS2=32,39,32,39;RE=71;REF_strand=116,140;Strandbias_pval=1;AF=0.277344 GT:DR:DV 0/0:185:71 +chr20 43260043 19 N TTTTTTTTTTTTTTTT . STRANDBIAS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=43260045;STD_quant_start=0.000000;STD_quant_stop=5.176872;Kurtosis_quant_start=7.000000;Kurtosis_quant_stop=1.701010;SVTYPE=INS;SUPTYPE=AL;SVLEN=11;STRANDS=+-;STRANDS2=11,0,11,0;RE=11;REF_strand=102,428;Strandbias_pval=2.2125e-08;AF=0.0207547 GT:DR:DV 0/0:519:11 diff --git a/SVs_sniffles/vcf/54917_bodySnif.vcf b/SVs_sniffles/vcf/54917_bodySnif.vcf new file mode 100644 index 0000000..28f86b1 --- /dev/null +++ b/SVs_sniffles/vcf/54917_bodySnif.vcf @@ -0,0 +1,36 @@ +##fileformat=VCFv4.1 +##source=Sniffles +##fileDate=20210810:55:48 AMef_minus +##contig= +##ALT= +##ALT= +##ALT= +##ALT= +##ALT= +##ALT= +##FILTER= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##FORMAT= +##FORMAT= +##FORMAT= +#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT bamfilt/54917_f.bam diff --git a/SVs_sniffles/vcf/54917_promoterSnif.vcf b/SVs_sniffles/vcf/54917_promoterSnif.vcf new file mode 100644 index 0000000..79cd62f --- /dev/null +++ b/SVs_sniffles/vcf/54917_promoterSnif.vcf @@ -0,0 +1,104 @@ +##fileformat=VCFv4.1 +##source=Sniffles +##fileDate=20210811:25:09 AMef_minus +##contig= +##ALT= +##ALT= +##ALT= +##ALT= +##ALT= +##ALT= +##FILTER= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##FORMAT= +##FORMAT= +##FORMAT= +#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT promoterbamfilt/54917_f.bam +chr20 4685096 0 CTCCTCTGTGCATTCTC N . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4685112;STD_quant_start=2.358495;STD_quant_stop=2.358495;Kurtosis_quant_start=-1.560987;Kurtosis_quant_stop=-1.176412;SVTYPE=DEL;SUPTYPE=AL;SVLEN=-16;STRANDS=+-;STRANDS2=26,7,26,7;RE=33;REF_strand=220279,32750;Strandbias_pval=0.187156;AF=0.00013042 GT:DR:DV 0/0:252996:33 +chr20 4685224 1 TTTTTTTTTTT N . STRANDBIAS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4685235;STD_quant_start=0.000000;STD_quant_stop=0.664074;Kurtosis_quant_start=1.934813;Kurtosis_quant_stop=3.075811;SVTYPE=DEL;SUPTYPE=AL;SVLEN=-11;STRANDS=+-;STRANDS2=810,156,810,156;RE=966;REF_strand=220634,32961;Strandbias_pval=0.00465183;AF=0.00380922 GT:DR:DV 0/0:252629:966 +chr20 4685224 2 N TTTTTTTTTTTTTTT . STRANDBIAS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4685224;STD_quant_start=0.000000;STD_quant_stop=1.189909;Kurtosis_quant_start=55.772243;Kurtosis_quant_stop=1.671801;SVTYPE=INS;SUPTYPE=AL;SVLEN=11;STRANDS=+-;STRANDS2=8654,60,8654,60;RE=8714;REF_strand=220628,32952;Strandbias_pval=0;AF=0.0343639 GT:DR:DV 0/0:244866:8714 +chr20 4685224 3 TTTTTTTTTTTG N . STRANDBIAS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4685241;STD_quant_start=2.652741;STD_quant_stop=2.136543;Kurtosis_quant_start=-1.207160;Kurtosis_quant_stop=0.047147;SVTYPE=DEL;SUPTYPE=AL,NR;SVLEN=-17;STRANDS=+-;STRANDS2=147,69,147,69;RE=216;REF_strand=220640,32964;Strandbias_pval=5.53829e-13;AF=0.000851722 GT:DR:DV 0/0:253388:216 +chr20 4685337 4 N CACACACACACACCACCCCACACACG . PASS IMPRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4685349;STD_quant_start=9.288311;STD_quant_stop=12.347248;Kurtosis_quant_start=-2.074860;Kurtosis_quant_stop=-2.069257;SVTYPE=INS;SUPTYPE=AL;SVLEN=11;STRANDS=+-;STRANDS2=21,1,21,1;RE=22;REF_strand=220742,33099;Strandbias_pval=0.34864;AF=8.66684e-05 GT:DR:DV 0/0:253819:22 +chr20 4685414 5 TTTTTTTATTTTTTGTAGAAATGGGGTCTCACTATGTTGCTCACTCTGGTCTCAAACTCC N . PASS IMPRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4685474;STD_quant_start=18.248288;STD_quant_stop=17.242390;Kurtosis_quant_start=-0.530343;Kurtosis_quant_stop=0.115361;SVTYPE=DEL;SUPTYPE=AL,NR;SVLEN=-60;STRANDS=+-;STRANDS2=11,0,11,0;RE=11;REF_strand=220750,33162;Strandbias_pval=0.379347;AF=4.33221e-05 GT:DR:DV 0/0:253901:11 +chr20 4685413 6 N TTTTTTTATTTT . STRANDBIAS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4685413;STD_quant_start=0.000000;STD_quant_stop=5.607383;Kurtosis_quant_start=1.996218;Kurtosis_quant_stop=-0.790914;SVTYPE=INS;SUPTYPE=AL;SVLEN=11;STRANDS=+-;STRANDS2=253,9,253,9;RE=262;REF_strand=220748,33136;Strandbias_pval=1.7181e-07;AF=0.00103197 GT:DR:DV 0/0:253622:262 +chr20 4685441 7 ATGTTGCTCACTCTGGTCTCAAACTCCTGA N . PASS IMPRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4685477;STD_quant_start=18.631125;STD_quant_stop=13.645077;Kurtosis_quant_start=-2.002936;Kurtosis_quant_stop=-1.912267;SVTYPE=DEL;SUPTYPE=AL;SVLEN=-36;STRANDS=+-;STRANDS2=165,38,165,38;RE=203;REF_strand=220750,33178;Strandbias_pval=0.0214998;AF=0.000799439 GT:DR:DV 0/0:253725:203 +chr20 4685510 8 CTCTGAAAGTGCTGGGATTACAGGCCTGAGCCACTGCACCTGGCTGTCA N . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4685549;STD_quant_start=4.669047;STD_quant_stop=8.916277;Kurtosis_quant_start=2.458911;Kurtosis_quant_stop=0.735266;SVTYPE=DEL;SUPTYPE=AL,NR;SVLEN=-39;STRANDS=+-;STRANDS2=9,3,9,3;RE=12;REF_strand=220754,33240;Strandbias_pval=0.200506;AF=4.72452e-05 GT:DR:DV 0/0:253982:12 +chr20 4685555 9 N TTTTTTTTTTTT . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4685557;STD_quant_start=8.011356;STD_quant_stop=6.660603;Kurtosis_quant_start=-1.662374;Kurtosis_quant_stop=-1.456577;SVTYPE=INS;SUPTYPE=AL;SVLEN=12;STRANDS=+-;STRANDS2=19,3,19,3;RE=22;REF_strand=220756,33271;Strandbias_pval=1;AF=8.6605e-05 GT:DR:DV 0/0:254005:22 +chr20 4685589 10 N TTATATTGCTTGTTTTGCTCCATA . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4685601;STD_quant_start=4.123106;STD_quant_stop=8.402381;Kurtosis_quant_start=-1.315544;Kurtosis_quant_stop=-1.394142;SVTYPE=INS;SUPTYPE=AL;SVLEN=11;STRANDS=+-;STRANDS2=14,6,14,6;RE=20;REF_strand=220757,33294;Strandbias_pval=0.038293;AF=7.87244e-05 GT:DR:DV 0/0:254031:20 +chr20 4685689 11 AGATCCCCCTCCCTCTAAATCCTGTC N . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4685715;STD_quant_start=7.705340;STD_quant_stop=9.640623;Kurtosis_quant_start=-1.848450;Kurtosis_quant_stop=-1.783157;SVTYPE=DEL;SUPTYPE=AL;SVLEN=-26;STRANDS=+-;STRANDS2=224,51,224,51;RE=275;REF_strand=220760,33410;Strandbias_pval=0.0120433;AF=0.00108195 GT:DR:DV 0/0:253895:275 +chr20 4685683 12 N TAATGTGAATAGGTCGGGAATAGGAAT . PASS IMPRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4685686;STD_quant_start=11.117554;STD_quant_stop=12.037442;Kurtosis_quant_start=-0.673438;Kurtosis_quant_stop=1.197983;SVTYPE=INS;SUPTYPE=AL;SVLEN=20;STRANDS=+-;STRANDS2=8,2,8,2;RE=10;REF_strand=220760,33391;Strandbias_pval=0.630174;AF=3.93467e-05 GT:DR:DV 0/0:254141:10 +chr20 4685835 13 N TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT . STRANDBIAS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4685851;STD_quant_start=2.020726;STD_quant_stop=7.228416;Kurtosis_quant_start=-0.254379;Kurtosis_quant_stop=-1.039963;SVTYPE=INS;SUPTYPE=AL;SVLEN=11;STRANDS=+-;STRANDS2=48,0,48,0;RE=48;REF_strand=220763,33527;Strandbias_pval=0.00205946;AF=0.000188761 GT:DR:DV 0/0:254242:48 +chr20 4685861 14 TTTGTTAATATCACCACCTAAATCATCTCTTG N . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4685895;STD_quant_start=4.224471;STD_quant_stop=5.255034;Kurtosis_quant_start=-0.412535;Kurtosis_quant_stop=-1.459156;SVTYPE=DEL;SUPTYPE=AL;SVLEN=-34;STRANDS=+-;STRANDS2=22,4,22,4;RE=26;REF_strand=220765,33553;Strandbias_pval=0.769446;AF=0.000102234 GT:DR:DV 0/0:254292:26 +chr20 4685930 15 AGGTGATGGTCAGTGTCCTT N . STRANDBIAS IMPRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4685951;STD_quant_start=10.732417;STD_quant_stop=10.624520;Kurtosis_quant_start=-1.875765;Kurtosis_quant_stop=-1.724715;SVTYPE=DEL;SUPTYPE=AL;SVLEN=-21;STRANDS=+-;STRANDS2=144,41,144,41;RE=185;REF_strand=220750,33605;Strandbias_pval=0.000992716;AF=0.00072733 GT:DR:DV 0/0:254170:185 +chr20 4686021 16 N TTTTTTTTTTTTTTT . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4686021;STD_quant_start=4.768556;STD_quant_stop=6.114843;Kurtosis_quant_start=-1.547274;Kurtosis_quant_stop=-1.692003;SVTYPE=INS;SUPTYPE=AL;SVLEN=13;STRANDS=+-;STRANDS2=42,4,42,4;RE=46;REF_strand=220346,33686;Strandbias_pval=0.512943;AF=0.00018108 GT:DR:DV 0/0:253986:46 +chr20 4686090 17 N TTTTTTTTTTTTTTTTTTTTTTTTT . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4686100;STD_quant_start=7.254309;STD_quant_stop=8.587782;Kurtosis_quant_start=-1.749448;Kurtosis_quant_stop=-1.651352;SVTYPE=INS;SUPTYPE=AL;SVLEN=11;STRANDS=+-;STRANDS2=32,0,32,0;RE=32;REF_strand=219972,33752;Strandbias_pval=0.0172204;AF=0.000126121 GT:DR:DV 0/0:253692:32 +chr20 4686080 18 TTCCTGAGCCT N . STRANDBIAS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4686091;STD_quant_start=3.888254;STD_quant_stop=4.622009;Kurtosis_quant_start=-0.981740;Kurtosis_quant_stop=-1.132825;SVTYPE=DEL;SUPTYPE=AL;SVLEN=-11;STRANDS=+-;STRANDS2=253,17,253,17;RE=270;REF_strand=220014,33743;Strandbias_pval=0.000306403;AF=0.00106401 GT:DR:DV 0/0:253487:270 +chr20 4686116 19 AAGATGATTTT N . STRANDBIAS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4686158;STD_quant_start=5.996527;STD_quant_stop=6.113510;Kurtosis_quant_start=-1.833754;Kurtosis_quant_stop=-1.835664;SVTYPE=DEL;SUPTYPE=AL;SVLEN=-42;STRANDS=+-;STRANDS2=33,15,33,15;RE=48;REF_strand=219679,33789;Strandbias_pval=0.00104798;AF=0.000189373 GT:DR:DV 0/0:253420:48 +chr20 4686249 20 N TTTTTTTTTTTTTTTTTTT . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4686249;STD_quant_start=0.242536;STD_quant_stop=2.828427;Kurtosis_quant_start=-0.800095;Kurtosis_quant_stop=-1.169825;SVTYPE=INS;SUPTYPE=AL;SVLEN=13;STRANDS=+-;STRANDS2=34,1,34,1;RE=35;REF_strand=218794,33882;Strandbias_pval=0.0791504;AF=0.000138517 GT:DR:DV 0/0:252641:35 +chr20 4686292 21 ACCCTTTAACTTAAA N . STRANDBIAS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4686304;STD_quant_start=4.872704;STD_quant_stop=4.426578;Kurtosis_quant_start=-1.964632;Kurtosis_quant_stop=0.472088;SVTYPE=DEL;SUPTYPE=AL,NR;SVLEN=-12;STRANDS=+-;STRANDS2=110,39,110,39;RE=149;REF_strand=218202,33911;Strandbias_pval=3.29173e-05;AF=0.000591005 GT:DR:DV 0/0:251964:149 +chr20 4686305 22 N ATTTTTCTATTTT . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4686308;STD_quant_start=5.253570;STD_quant_stop=6.041523;Kurtosis_quant_start=-1.531631;Kurtosis_quant_stop=-1.654718;SVTYPE=INS;SUPTYPE=AL;SVLEN=11;STRANDS=+-;STRANDS2=21,0,21,0;RE=21;REF_strand=218126,33918;Strandbias_pval=0.101466;AF=8.33188e-05 GT:DR:DV 0/0:252023:21 +chr20 4686326 23 GGGGGCACAGAGTGTGCGCCGGGCCGCGCGGCAATTGGTCCCCGCGCCGACCTCCGCCCGCGAGCGCCGCCGCTTCCCTTCCCCGCCCCGCGTCCCTCCCCCTCGGCCCCGCGCGTCGCCTGTCCTCCGAGCCAGTCGCTGACAGCCGCGGCGCCGCGAGCTTCTCCTCTCCTCACGACCGAGGCAGGTAAACGCCCGGGGTGGGAGGAACGCGGGCGGGGGCAGGGGAGCCGCGGGGGCCGAGTGAGGACCCCGGGCCTCGGGTCCCAGGCGCAAGGGTGCCCGGCCGGGCGGGGTCGGGACCCCAGTGAGGAGGGGCCGGGGGCTGCCCCGCGGGCGCGTGACGCGTCTCGGGCCTGCCCGGCTGCGCTGGTCTCCGCTCGGGTGAGGCGGCTTGGCTTCGCTTTTCAGGTTAGGAAAGCTCCCTTTACTGCGCGTTGGGGGGCTGGGGGAGCTGGCGGAGCCCCGTTAGGGAGGTCGGTGGCGCCGGGGTGTCTCAGCGCCCCCTGCACCCCGCGCGGGTCCGGCCCAGCGGGCGATCGCTGGCGCCCAGGGAACTCCGGGAGGGCCGCCAGCGGGCTCCGCAGGGCGCGGGGCGGGGAGGGGCGCCTGGGGGCCGCGGGGCTCGCGCTCCCCGCCCGTTGGCCGCCCCTCGGAGGCCGAGATCGGGGCCCAGAACGCCCCTTGGCAAGGCCTGGCGCTTCCGCGATGCCCAGAGGGTGCTTGGGGGGATGGAGAGAGGGGCGCCCGCCG N . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4687079;STD_quant_start=0.447214;STD_quant_stop=0.836660;Kurtosis_quant_start=4.918197;Kurtosis_quant_stop=1.871166;SVTYPE=DEL;SUPTYPE=AL,NR;SVLEN=-753;STRANDS=+-;STRANDS2=14,2,14,2;RE=16;REF_strand=215508,34284;Strandbias_pval=1;AF=6.40533e-05 GT:DR:DV 0/0:249776:16 +chr20 4686364 24 GCCGACCTCCGCCCGCGAGCGCCGCCGCTTCCCTTCCCCGCCCCGCGTCCCTCCCCCT N . PASS IMPRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4686435;STD_quant_start=4.571652;STD_quant_stop=15.329710;Kurtosis_quant_start=-1.153761;Kurtosis_quant_stop=-1.864057;SVTYPE=DEL;SUPTYPE=AL,NR;SVLEN=-71;STRANDS=+-;STRANDS2=17,3,17,3;RE=20;REF_strand=217421,33982;Strandbias_pval=0.745741;AF=7.95535e-05 GT:DR:DV 0/0:251383:20 +chr20 4686367 25 N GCCCCGCTTCA . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4686378;STD_quant_start=5.854291;STD_quant_stop=8.235180;Kurtosis_quant_start=-1.770078;Kurtosis_quant_stop=-1.684523;SVTYPE=INS;SUPTYPE=AL;SVLEN=12;STRANDS=+-;STRANDS2=21,1,21,1;RE=22;REF_strand=217621,33965;Strandbias_pval=0.348973;AF=8.74452e-05 GT:DR:DV 0/0:251564:22 +chr20 4686407 26 N ACAACGCACGCGCACACG . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4686407;STD_quant_start=5.291503;STD_quant_stop=6.592006;Kurtosis_quant_start=-1.584331;Kurtosis_quant_stop=-1.583052;SVTYPE=INS;SUPTYPE=AL;SVLEN=25;STRANDS=+-;STRANDS2=20,2,20,2;RE=22;REF_strand=217338,33986;Strandbias_pval=0.759082;AF=8.75364e-05 GT:DR:DV 0/0:251302:22 +chr20 4686395 27 TTCCCCGCCCCGCGTCCCTCCCCCTCGGCCCCG N . STRANDBIAS IMPRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4686437;STD_quant_start=7.225343;STD_quant_stop=12.560932;Kurtosis_quant_start=-0.835910;Kurtosis_quant_stop=-2.029072;SVTYPE=DEL;SUPTYPE=AL,NR;SVLEN=-42;STRANDS=+-;STRANDS2=440,134,440,134;RE=574;REF_strand=217297,33994;Strandbias_pval=2.12131e-10;AF=0.0022842 GT:DR:DV 0/0:250717:574 +chr20 4686486 28 CTTCTCCTCTC N . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4686501;STD_quant_start=1.653946;STD_quant_stop=2.620643;Kurtosis_quant_start=1.032537;Kurtosis_quant_stop=1.026529;SVTYPE=DEL;SUPTYPE=AL,NR;SVLEN=-15;STRANDS=+-;STRANDS2=215,28,215,28;RE=243;REF_strand=216767,34060;Strandbias_pval=0.39906;AF=0.000968795 GT:DR:DV 0/0:250584:243 +chr20 4686485 29 GCTTCTCCTCTCCTCACGACCGAGGCAGGTAAACGCCCGGGGTGGGAGGAACGCGGGCGGGGGCAGGGGAGC N . PASS IMPRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4686571;STD_quant_start=12.903488;STD_quant_stop=16.385970;Kurtosis_quant_start=1.507052;Kurtosis_quant_stop=-1.302422;SVTYPE=DEL;SUPTYPE=AL;SVLEN=-86;STRANDS=+-;STRANDS2=7,4,7,4;RE=11;REF_strand=216530,34095;Strandbias_pval=0.0511519;AF=4.38903e-05 GT:DR:DV 0/0:250614:11 +chr20 4686538 30 GGGGGCAGGGGAGCCGCGGGGGCCGAGTGAGGACCCCGGGCCTCGGGTCCCAGGCGCAAGGGTGCCCGGCCGGGCGGGGTCGGGACCCCAGTGAGGAGGGGCCGGGGGCTGCCCCGCGGGCGCGTGACGCGTCTCGGGCCTGCCCGGCTGCGCTGGTCTCCGCTCGGGTGAGGCGGCTTGGCTTCGCTTTTCAGGTTAGGAAAGCTCCCTTTACTGCGCGTTGGGGGGCTGGGGGAGCTGGCGGAGCCCCGTTAGGGAGGTCGGTGGCGCCGGGGTGTCTCAGCGCCCCCTGCACCCCGCGCGGGTCCGGCCCAGCGGGCGATCGCTGGCGCCCAGGGAACTCCGGGAGGGCCGCCAGCGGGCTCCGCAGGGCGCGGGGCGGGGAGGGGCGCCTGGGGGCCGCGGGGCTCGCGCTCCCCGCCCGTTGGCCGCCCCTCGGAGGCCGAGATCGGGGCCCAGAACGCCCCTTGGCAAGGCCTGGCGCTTCCGCGATGCCCAGAGGGTGCTTGGGGGGATGGAGAGAGGGGCGCCCGCCGGGGGAGTTCCGGGAGCCTCGGTGCCTCCCGCCGCAGCTGCAGCGTTCCTCCCGGGAGGCGGCCCAGCCCTTCATCCTCGCCGCCTGAGCTTCTCCGAGGGGGGCTGCAGCCTTGCGGCCGTTGCCACCGCCTGGAGAAGCGGCCCACGCGGACTGA N . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4687235;STD_quant_start=2.614065;STD_quant_stop=3.500000;Kurtosis_quant_start=-0.515707;Kurtosis_quant_stop=-1.216969;SVTYPE=DEL;SUPTYPE=AL;SVLEN=-697;STRANDS=+-;STRANDS2=21,3,21,3;RE=24;REF_strand=214278,34388;Strandbias_pval=1;AF=9.6515e-05 GT:DR:DV 0/0:248642:24 +chr20 4686617 31 CGGGGTCGGGA N . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4686628;STD_quant_start=5.284229;STD_quant_stop=4.042358;Kurtosis_quant_start=-0.267454;Kurtosis_quant_stop=-1.827076;SVTYPE=DEL;SUPTYPE=AL;SVLEN=-11;STRANDS=+-;STRANDS2=146,37,146,37;RE=183;REF_strand=216010,34191;Strandbias_pval=0.0130496;AF=0.000731412 GT:DR:DV 0/0:250018:183 +chr20 4686576 32 N CCCCCGCTGCC . PASS IMPRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4686586;STD_quant_start=11.674759;STD_quant_stop=9.989995;Kurtosis_quant_start=-0.692222;Kurtosis_quant_stop=-1.521756;SVTYPE=INS;SUPTYPE=AL;SVLEN=11;STRANDS=+-;STRANDS2=14,4,14,4;RE=18;REF_strand=216201,34155;Strandbias_pval=0.295118;AF=7.18976e-05 GT:DR:DV 0/0:250338:18 +chr20 4686597 33 GCAAGGGTGCCCGGCCGGGCGGGGTCGGGACCCCAGTGAGGAGGGGCCGGGGGCTGCCCCGCGGGCGCG N . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4686668;STD_quant_start=9.253992;STD_quant_stop=7.810250;Kurtosis_quant_start=-2.187138;Kurtosis_quant_stop=-1.125318;SVTYPE=DEL;SUPTYPE=AL,NR;SVLEN=-71;STRANDS=+-;STRANDS2=16,7,16,7;RE=23;REF_strand=215922,34208;Strandbias_pval=0.029695;AF=9.19522e-05 GT:DR:DV 0/0:250107:23 +chr20 4686641 34 N AGCCGGCGCAGCTGCGCGCT . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4686646;STD_quant_start=7.507572;STD_quant_stop=6.915069;Kurtosis_quant_start=-1.598675;Kurtosis_quant_stop=-1.684890;SVTYPE=INS;SUPTYPE=AL;SVLEN=11;STRANDS=+-;STRANDS2=20,2,20,2;RE=22;REF_strand=215889,34216;Strandbias_pval=0.759057;AF=8.79631e-05 GT:DR:DV 0/0:250083:22 +chr20 4686720 35 TTGGCTTCGCT N . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4686734;STD_quant_start=1.434860;STD_quant_stop=1.925067;Kurtosis_quant_start=-0.048454;Kurtosis_quant_stop=0.089844;SVTYPE=DEL;SUPTYPE=AL,NR;SVLEN=-14;STRANDS=+-;STRANDS2=54,14,54,14;RE=68;REF_strand=215288,34306;Strandbias_pval=0.111295;AF=0.000272442 GT:DR:DV 0/0:249526:68 +chr20 4686765 36 GGGGGGCTGGGGG N . STRANDBIAS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4686779;STD_quant_start=7.027595;STD_quant_stop=6.036181;Kurtosis_quant_start=-1.840058;Kurtosis_quant_stop=-1.551713;SVTYPE=DEL;SUPTYPE=AL;SVLEN=-14;STRANDS=+-;STRANDS2=78,46,78,46;RE=124;REF_strand=214997,34351;Strandbias_pval=7.95578e-11;AF=0.000497297 GT:DR:DV 0/0:249224:124 +chr20 4686795 37 N GGGGGGGGGGG . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4686803;STD_quant_start=8.142481;STD_quant_stop=9.648834;Kurtosis_quant_start=-0.918704;Kurtosis_quant_stop=0.533290;SVTYPE=INS;SUPTYPE=AL;SVLEN=11;STRANDS=+-;STRANDS2=8,4,8,4;RE=12;REF_strand=214817,34375;Strandbias_pval=0.0716821;AF=4.81556e-05 GT:DR:DV 0/0:249180:12 +chr20 4686815 38 GGGTGTCTCAGCGCCCCCTGCACCCCGCGCGGGTCCGGCCCAGCGGGCGATCGCTGGCGCCCAGGGAACTCCGGGAGGGCCGCCAGCGGGCTCCGCAGGGCGCGGGGCGGGGAGGGGCGCCT N . PASS IMPRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4686943;STD_quant_start=4.195235;STD_quant_stop=10.959015;Kurtosis_quant_start=2.385437;Kurtosis_quant_stop=-0.456268;SVTYPE=DEL;SUPTYPE=AL;SVLEN=-128;STRANDS=+-;STRANDS2=11,2,11,2;RE=13;REF_strand=214318,34441;Strandbias_pval=0.698978;AF=5.22594e-05 GT:DR:DV 0/0:248746:13 +chr20 4686945 39 CGGGGCTCGCGCTCCCCGCCCGTTGGCCGCC N . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4686975;STD_quant_start=4.026697;STD_quant_stop=1.945691;Kurtosis_quant_start=-1.053463;Kurtosis_quant_stop=-0.857252;SVTYPE=DEL;SUPTYPE=AL;SVLEN=-30;STRANDS=+-;STRANDS2=24,5,24,5;RE=29;REF_strand=213814,34514;Strandbias_pval=0.589274;AF=0.000116781 GT:DR:DV 0/0:248299:29 +chr20 4686928 40 GGGCGCCTGGGGGCCGCGGGGCTC N . STRANDBIAS IMPRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4686953;STD_quant_start=10.320160;STD_quant_stop=10.331207;Kurtosis_quant_start=-1.691326;Kurtosis_quant_stop=-1.716800;SVTYPE=DEL;SUPTYPE=AL;SVLEN=-25;STRANDS=+-;STRANDS2=360,166,360,166;RE=526;REF_strand=213930,34496;Strandbias_pval=3.80886e-25;AF=0.00211733 GT:DR:DV 0/0:247900:526 +chr20 4686961 41 N GCCCAGCCCTT . PASS IMPRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4686971;STD_quant_start=10.002272;STD_quant_stop=5.869799;Kurtosis_quant_start=-1.831834;Kurtosis_quant_stop=-1.778421;SVTYPE=INS;SUPTYPE=AL;SVLEN=11;STRANDS=+-;STRANDS2=41,4,41,4;RE=45;REF_strand=213769,34527;Strandbias_pval=0.515087;AF=0.000181235 GT:DR:DV 0/0:248251:45 +chr20 4686949 42 GGCTCGCGCTCCCCGCCCGTTGGCCGCCCCTCGGAGGCCGAGATCGGGGCCCAGAACGCCCCTTGGCAAGGCCTGGCGCTTCCGCGATGCCCAGAGGGTGCTTGGGGGGATGGAGAGAGGGGCGCCCGCCGGGGGAGTTCCGGGAGCCTCGGTGCCTCCCGCCGCAGCTGCAGCGTT N . PASS IMPRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4687086;STD_quant_start=16.816658;STD_quant_stop=26.296388;Kurtosis_quant_start=-0.123561;Kurtosis_quant_stop=-1.497561;SVTYPE=DEL;SUPTYPE=AL;SVLEN=-137;STRANDS=+-;STRANDS2=11,1,11,1;RE=12;REF_strand=213447,34572;Strandbias_pval=1;AF=4.83834e-05 GT:DR:DV 0/0:248007:12 +chr20 4687051 43 GGGGGGATGGAGA N . STRANDBIAS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4687064;STD_quant_start=1.481063;STD_quant_stop=2.221595;Kurtosis_quant_start=0.384011;Kurtosis_quant_stop=-1.250884;SVTYPE=DEL;SUPTYPE=AL,NR;SVLEN=-13;STRANDS=+-;STRANDS2=33,29,33,29;RE=62;REF_strand=213223,34611;Strandbias_pval=5.63404e-10;AF=0.000250167 GT:DR:DV 0/0:247772:62 +chr20 4687032 44 N ACCGCCGCAGCC . PASS IMPRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4687040;STD_quant_start=7.563068;STD_quant_stop=10.183320;Kurtosis_quant_start=-0.679339;Kurtosis_quant_stop=-1.643475;SVTYPE=INS;SUPTYPE=AL;SVLEN=12;STRANDS=+-;STRANDS2=20,0,20,0;RE=20;REF_strand=213337,34602;Strandbias_pval=0.0994696;AF=8.0665e-05 GT:DR:DV 0/0:247919:20 +chr20 4687051 45 N GGGGGGGGGGGGGGGGG . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4687062;STD_quant_start=1.087115;STD_quant_stop=6.396021;Kurtosis_quant_start=-0.901942;Kurtosis_quant_stop=-0.428137;SVTYPE=INS;SUPTYPE=AL;SVLEN=11;STRANDS=+-;STRANDS2=19,4,19,4;RE=23;REF_strand=213227,34611;Strandbias_pval=0.552259;AF=9.28026e-05 GT:DR:DV 0/0:247815:23 +chr20 4687212 46 GAGAAGCGGCCCAC N . STRANDBIAS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4687226;STD_quant_start=2.800162;STD_quant_stop=3.677326;Kurtosis_quant_start=1.215040;Kurtosis_quant_stop=-1.599749;SVTYPE=DEL;SUPTYPE=AL;SVLEN=-14;STRANDS=+-;STRANDS2=87,1,87,1;RE=88;REF_strand=212215,34670;Strandbias_pval=4.19585e-05;AF=0.000356441 GT:DR:DV 0/0:246797:88 +chr20 4687223 47 CACGCGGACTGA N . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4687235;STD_quant_start=1.414214;STD_quant_stop=1.375811;Kurtosis_quant_start=0.047088;Kurtosis_quant_stop=0.609716;SVTYPE=DEL;SUPTYPE=AL;SVLEN=-12;STRANDS=+-;STRANDS2=48,8,48,8;RE=56;REF_strand=212145,34670;Strandbias_pval=1;AF=0.000226891 GT:DR:DV 0/0:246759:56 +chr20 4687231 48 N CGGCGCGCTTTG . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4687233;STD_quant_start=5.709641;STD_quant_stop=7.056912;Kurtosis_quant_start=-1.452332;Kurtosis_quant_stop=-0.711242;SVTYPE=INS;SUPTYPE=AL;SVLEN=12;STRANDS=+-;STRANDS2=15,1,15,1;RE=16;REF_strand=212141,34670;Strandbias_pval=0.715542;AF=6.48269e-05 GT:DR:DV 0/0:246795:16 +chr20 4687236 49 GGCGGGGGCGGGGCCTCGGGCCTCGGCGGGGGCGGGGTCCGGGGAGGCCCCACCCTCTGTTCTCCAGGGGCGGGGAGAGAGGAGCTGCAGGTCTGCGGCCTGGCCCCAGGTGCGATGGCGGACCCCAGCTTGGCCAGTCACATTCCTCCCAGTCCCCCTGGAGGGAGAACGCTGGCCATGGGGGGCTCCA N . PASS IMPRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4687427;STD_quant_start=19.728152;STD_quant_stop=19.636700;Kurtosis_quant_start=-1.151031;Kurtosis_quant_stop=2.358833;SVTYPE=DEL;SUPTYPE=AL;SVLEN=-191;STRANDS=+-;STRANDS2=9,1,9,1;RE=10;REF_strand=211554,34670;Strandbias_pval=1;AF=4.06134e-05 GT:DR:DV 0/0:246214:10 +chr20 4687275 50 CCGGGGAGGCCCC N . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4687289;STD_quant_start=6.043154;STD_quant_stop=6.239079;Kurtosis_quant_start=-1.606451;Kurtosis_quant_stop=-1.710716;SVTYPE=DEL;SUPTYPE=AL,NR;SVLEN=-14;STRANDS=+-;STRANDS2=677,136,677,136;RE=813;REF_strand=211757,34670;Strandbias_pval=0.0337255;AF=0.00329915 GT:DR:DV 0/0:245614:813 +chr20 4687263 51 CGGGGGCGGGGTCCGGGGAGGCCCCACCCTCTGTTCTCCAGGGGCGGGGAGAGAGGAGCTGCAGGTCTGCGGCCTGGCCCCAGGTGCGATGGCGGA N . PASS IMPRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4687368;STD_quant_start=14.741099;STD_quant_stop=18.094198;Kurtosis_quant_start=-0.420545;Kurtosis_quant_stop=-1.348355;SVTYPE=DEL;SUPTYPE=AL;SVLEN=-105;STRANDS=+-;STRANDS2=10,2,10,2;RE=12;REF_strand=211628,34670;Strandbias_pval=0.681647;AF=4.87215e-05 GT:DR:DV 0/0:246286:12 +chr20 4687349 52 CGATGGCGGACCC N . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4687367;STD_quant_start=6.864919;STD_quant_stop=6.171971;Kurtosis_quant_start=-0.597465;Kurtosis_quant_stop=-0.202177;SVTYPE=DEL;SUPTYPE=AL,NR;SVLEN=-18;STRANDS=+-;STRANDS2=212,24,212,24;RE=236;REF_strand=211361,34670;Strandbias_pval=0.091514;AF=0.000959229 GT:DR:DV 0/0:245795:236 +chr20 4687370 53 GCCAGTCACATTCC N . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4687383;STD_quant_start=1.017095;STD_quant_stop=1.450327;Kurtosis_quant_start=-0.169255;Kurtosis_quant_stop=0.580743;SVTYPE=DEL;SUPTYPE=AL;SVLEN=-13;STRANDS=+-;STRANDS2=56,3,56,3;RE=59;REF_strand=211278,34670;Strandbias_pval=0.0580432;AF=0.000239888 GT:DR:DV 0/0:245889:59 +chr20 4687442 54 CTCGGATGACGACCCTTGGGTCACCGGTCTCCCCACCTG N . PASS IMPRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4687484;STD_quant_start=14.733183;STD_quant_stop=10.395512;Kurtosis_quant_start=-1.784038;Kurtosis_quant_stop=-1.920867;SVTYPE=DEL;SUPTYPE=AL,NR;SVLEN=-42;STRANDS=+-;STRANDS2=292,39,292,39;RE=331;REF_strand=210861,34669;Strandbias_pval=0.236726;AF=0.0013481 GT:DR:DV 0/0:245199:331 +chr20 4687466 55 GGCAGGCGCCTTCACGTTTCATTATTAAACAATGGGGAGAAATCCATGTTTACTGTCCTTTTTAAGGAATTTTTTGCTCTTCTCTTTGA N . PASS IMPRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4687571;STD_quant_start=12.853015;STD_quant_stop=13.296616;Kurtosis_quant_start=-1.201034;Kurtosis_quant_stop=-1.043602;SVTYPE=DEL;SUPTYPE=AL;SVLEN=-105;STRANDS=+-;STRANDS2=10,2,10,2;RE=12;REF_strand=210560,34666;Strandbias_pval=0.682735;AF=4.89345e-05 GT:DR:DV 0/0:245214:12 +chr20 4687540 56 TTTTTAAGGAA N . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4687552;STD_quant_start=3.894440;STD_quant_stop=5.004165;Kurtosis_quant_start=-1.082883;Kurtosis_quant_stop=-0.881757;SVTYPE=DEL;SUPTYPE=AL;SVLEN=-12;STRANDS=+-;STRANDS2=131,14,131,14;RE=145;REF_strand=210364,34666;Strandbias_pval=0.15117;AF=0.000591764 GT:DR:DV 0/0:244885:145 +chr20 4687590 57 N TTTTTTTTTTTTTTTT . STRANDBIAS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4687591;STD_quant_start=0.000000;STD_quant_stop=3.427112;Kurtosis_quant_start=-1.296875;Kurtosis_quant_stop=-0.947402;SVTYPE=INS;SUPTYPE=AL;SVLEN=11;STRANDS=+-;STRANDS2=99,3,99,3;RE=102;REF_strand=210091,34664;Strandbias_pval=0.000297619;AF=0.000416743 GT:DR:DV 0/0:244653:102 +chr20 4687589 58 ATTTTTTTTTTAA N . STRANDBIAS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4687602;STD_quant_start=6.906062;STD_quant_stop=7.254076;Kurtosis_quant_start=-1.575249;Kurtosis_quant_stop=-1.498530;SVTYPE=DEL;SUPTYPE=AL,NR;SVLEN=-13;STRANDS=+-;STRANDS2=173,49,173,49;RE=222;REF_strand=210088,34664;Strandbias_pval=0.0013946;AF=0.000907041 GT:DR:DV 0/0:244530:222 +chr20 4687590 59 N TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT . PASS IMPRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4687629;STD_quant_start=21.260292;STD_quant_stop=12.802344;Kurtosis_quant_start=-1.896151;Kurtosis_quant_stop=-1.898256;SVTYPE=INS;SUPTYPE=AL;SVLEN=11;STRANDS=+-;STRANDS2=16,1,16,1;RE=17;REF_strand=210006,34664;Strandbias_pval=0.496211;AF=6.94813e-05 GT:DR:DV 0/0:244653:17 +chr20 4687660 60 N TTTTTTTTTTT . PASS IMPRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4687687;STD_quant_start=6.329824;STD_quant_stop=15.813496;Kurtosis_quant_start=-1.795128;Kurtosis_quant_stop=-2.137968;SVTYPE=INS;SUPTYPE=AL;SVLEN=12;STRANDS=+-;STRANDS2=27,4,27,4;RE=31;REF_strand=209631,34662;Strandbias_pval=1;AF=0.000126897 GT:DR:DV 0/0:244262:31 +chr20 4687734 61 CCGCGTTATTTT N . STRANDBIAS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4687747;STD_quant_start=2.384474;STD_quant_stop=4.708655;Kurtosis_quant_start=-1.468230;Kurtosis_quant_stop=-1.659808;SVTYPE=DEL;SUPTYPE=AL;SVLEN=-13;STRANDS=+-;STRANDS2=69,1,69,1;RE=70;REF_strand=209217,34660;Strandbias_pval=0.000462772;AF=0.00028703 GT:DR:DV 0/0:243807:70 +chr20 4687765 62 GTTCCCCATATGATTT N . STRANDBIAS IMPRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4687797;STD_quant_start=12.341237;STD_quant_stop=8.786585;Kurtosis_quant_start=-2.013899;Kurtosis_quant_stop=-1.924433;SVTYPE=DEL;SUPTYPE=AL;SVLEN=-32;STRANDS=+-;STRANDS2=68,31,68,31;RE=99;REF_strand=208980,34660;Strandbias_pval=1.58349e-05;AF=0.000406337 GT:DR:DV 0/0:243541:99 +chr20 4687768 63 N ACACACAATGGAC . PASS IMPRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4687794;STD_quant_start=10.516653;STD_quant_stop=14.113823;Kurtosis_quant_start=-0.461882;Kurtosis_quant_stop=-1.618595;SVTYPE=INS;SUPTYPE=AL;SVLEN=13;STRANDS=+-;STRANDS2=11,3,11,3;RE=14;REF_strand=208982,34660;Strandbias_pval=0.437018;AF=5.74614e-05 GT:DR:DV 0/0:243628:14 +chr20 4687873 64 AAATCAACAACGCT N . STRANDBIAS IMPRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4687972;STD_quant_start=18.093434;STD_quant_stop=23.764357;Kurtosis_quant_start=-1.965977;Kurtosis_quant_stop=-2.027832;SVTYPE=DEL;SUPTYPE=AL;SVLEN=-99;STRANDS=+-;STRANDS2=146,42,146,42;RE=188;REF_strand=208132,34644;Strandbias_pval=0.00324153;AF=0.000774376 GT:DR:DV 0/0:242588:188 +chr20 4687964 65 N . PASS IMPRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4688005;STD_quant_start=10.397368;STD_quant_stop=7.163504;Kurtosis_quant_start=-1.940362;Kurtosis_quant_stop=-1.839432;SVTYPE=DEL;SUPTYPE=AL;SVLEN=-41;STRANDS=+-;STRANDS2=101,13,101,13;RE=114;REF_strand=207529,34606;Strandbias_pval=0.424537;AF=0.000470812 GT:DR:DV 0/0:242021:114 +chr20 4688017 66 N . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4688029;STD_quant_start=2.345208;STD_quant_stop=1.949359;Kurtosis_quant_start=-1.555832;Kurtosis_quant_stop=-1.794694;SVTYPE=DEL;SUPTYPE=AL;SVLEN=-12;STRANDS=+-;STRANDS2=9,5,9,5;RE=14;REF_strand=206004,34377;Strandbias_pval=0.0390009;AF=5.82409e-05 GT:DR:DV 0/0:240367:14 +chr20 4688011 67 N AAAAAAAAAAA . STRANDBIAS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4688011;STD_quant_start=0.000000;STD_quant_stop=2.213594;Kurtosis_quant_start=0.568432;Kurtosis_quant_stop=-0.310833;SVTYPE=INS;SUPTYPE=AL;SVLEN=11;STRANDS=+-;STRANDS2=7,12,7,12;RE=19;REF_strand=206862,34536;Strandbias_pval=1.38103e-06;AF=7.87082e-05 GT:DR:DV 0/0:241379:19 diff --git a/SVs_sniffles/vcf/54960_bodySnif.vcf b/SVs_sniffles/vcf/54960_bodySnif.vcf new file mode 100644 index 0000000..f78a5ca --- /dev/null +++ b/SVs_sniffles/vcf/54960_bodySnif.vcf @@ -0,0 +1,37 @@ +##fileformat=VCFv4.1 +##source=Sniffles +##fileDate=20210810:55:59 AMef_minus +##contig= +##ALT= +##ALT= +##ALT= +##ALT= +##ALT= +##ALT= +##FILTER= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##FORMAT= +##FORMAT= +##FORMAT= +#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT bamfilt/54960_f.bam +chr20 4701225 0 N AACGAAAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGA . PASS IMPRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4701238;STD_quant_start=25.680732;STD_quant_stop=22.761810;Kurtosis_quant_start=-1.063247;Kurtosis_quant_stop=-1.172800;SVTYPE=INS;SUPTYPE=AL;SVLEN=52;STRANDS=+-;STRANDS2=4,6,4,6;RE=10;REF_strand=11450,12582;Strandbias_pval=0.756582;AF=0.000416112 GT:DR:DV 0/0:24022:10 diff --git a/SVs_sniffles/vcf/54960_promoterSnif.vcf b/SVs_sniffles/vcf/54960_promoterSnif.vcf new file mode 100644 index 0000000..5799e5e --- /dev/null +++ b/SVs_sniffles/vcf/54960_promoterSnif.vcf @@ -0,0 +1,123 @@ +##fileformat=VCFv4.1 +##source=Sniffles +##fileDate=20210811:29:57 AMef_minus +##contig= +##ALT= +##ALT= +##ALT= +##ALT= +##ALT= +##ALT= +##FILTER= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##FORMAT= +##FORMAT= +##FORMAT= +#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT promoterbamfilt/54960_f.bam +chr20 4685094 0 TCTCCTCTGTGCAT N . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4685108;STD_quant_start=1.390444;STD_quant_stop=1.064581;Kurtosis_quant_start=-0.042979;Kurtosis_quant_stop=-0.365163;SVTYPE=DEL;SUPTYPE=AL;SVLEN=-14;STRANDS=+-;STRANDS2=13,17,13,17;RE=30;REF_strand=240752,240877;Strandbias_pval=0.584653;AF=6.22886e-05 GT:DR:DV 0/0:481599:30 +chr20 4685147 1 N GCCCCATATATTACCATACTTTGTACTATTCTGCC . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4685154;STD_quant_start=4.582576;STD_quant_stop=5.693564;Kurtosis_quant_start=-1.801808;Kurtosis_quant_stop=-1.891315;SVTYPE=INS;SUPTYPE=AL;SVLEN=11;STRANDS=+-;STRANDS2=12,12,12,12;RE=24;REF_strand=241084,241691;Strandbias_pval=1;AF=4.97126e-05 GT:DR:DV 0/0:482751:24 +chr20 4685224 2 TTTTTTTTTTTTTT N . STRANDBIAS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4685235;STD_quant_start=0.000000;STD_quant_stop=1.162523;Kurtosis_quant_start=2.917304;Kurtosis_quant_stop=3.988381;SVTYPE=DEL;SUPTYPE=AL,NR;SVLEN=-11;STRANDS=+-;STRANDS2=915,1072,915,1072;RE=1987;REF_strand=241166,242243;Strandbias_pval=0.000683926;AF=0.00411039 GT:DR:DV 0/0:481422:1987 +chr20 4685224 3 N TTTTTTTTTTTTT . STRANDBIAS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4685224;STD_quant_start=0.000000;STD_quant_stop=1.157899;Kurtosis_quant_start=45.702254;Kurtosis_quant_stop=1.723778;SVTYPE=INS;SUPTYPE=AL;SVLEN=11;STRANDS=+-;STRANDS2=7112,278,7112,278;RE=7390;REF_strand=241162,242206;Strandbias_pval=0;AF=0.0152886 GT:DR:DV 0/0:475978:7390 +chr20 4685224 4 TTTTTTTTTTTTTTTTGT N . STRANDBIAS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4685242;STD_quant_start=1.936492;STD_quant_stop=1.878238;Kurtosis_quant_start=-1.108098;Kurtosis_quant_stop=0.031266;SVTYPE=DEL;SUPTYPE=AL,NR;SVLEN=-18;STRANDS=+-;STRANDS2=124,236,124,236;RE=360;REF_strand=241173,242280;Strandbias_pval=3.80538e-09;AF=0.000744643 GT:DR:DV 0/0:483093:360 +chr20 4685224 5 ACAAAGAGTGAGACAGGGTCTTGGCCTATAGCCCTGTGGCCCAGGCTGGAGTGCAGTGGCACAATTAAAGCTCACTGCAGCCTCTACCTCCT N . PASS IMPRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4685333;STD_quant_start=9.444575;STD_quant_stop=19.097120;Kurtosis_quant_start=-0.662280;Kurtosis_quant_stop=-1.515217;SVTYPE=DEL;SUPTYPE=AL,NR;SVLEN=-109;STRANDS=+-;STRANDS2=2,10,2,10;RE=12;REF_strand=241217,242592;Strandbias_pval=0.0385811;AF=2.48032e-05 GT:DR:DV 0/0:483797:12 +chr20 4685262 6 AGGGTCTTGGCCTAT N . STRANDBIAS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4685275;STD_quant_start=4.497363;STD_quant_stop=5.271463;Kurtosis_quant_start=-1.410028;Kurtosis_quant_stop=-1.568695;SVTYPE=DEL;SUPTYPE=AL;SVLEN=-13;STRANDS=+-;STRANDS2=57,218,57,218;RE=275;REF_strand=241191,242513;Strandbias_pval=2.55591e-23;AF=0.00056853 GT:DR:DV 0/0:483429:275 +chr20 4685361 7 N CCCTTTTCCCC . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4685364;STD_quant_start=5.690748;STD_quant_stop=5.909575;Kurtosis_quant_start=-1.804153;Kurtosis_quant_stop=-1.871131;SVTYPE=INS;SUPTYPE=AL;SVLEN=11;STRANDS=+-;STRANDS2=16,10,16,10;RE=26;REF_strand=241283,243180;Strandbias_pval=0.246013;AF=5.36677e-05 GT:DR:DV 0/0:484437:26 +chr20 4685413 8 N TTTTTTTTTTT . STRANDBIAS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4685413;STD_quant_start=0.000000;STD_quant_stop=4.706842;Kurtosis_quant_start=1.365944;Kurtosis_quant_stop=-0.773090;SVTYPE=INS;SUPTYPE=AL;SVLEN=12;STRANDS=+-;STRANDS2=251,48,251,48;RE=299;REF_strand=241286,243454;Strandbias_pval=1.02454e-34;AF=0.000616826 GT:DR:DV 0/0:484441:299 +chr20 4685453 9 TCCTGAGCTCAAGCAATCT N . PASS IMPRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4685490;STD_quant_start=10.484848;STD_quant_stop=7.862903;Kurtosis_quant_start=-1.963783;Kurtosis_quant_stop=-1.855014;SVTYPE=DEL;SUPTYPE=AL;SVLEN=-37;STRANDS=+-;STRANDS2=107,100,107,100;RE=207;REF_strand=241289,243754;Strandbias_pval=0.579026;AF=0.000426766 GT:DR:DV 0/0:484836:207 +chr20 4685467 10 N AAAAAAAAAAAAAAAAA . PASS IMPRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4685487;STD_quant_start=3.009788;STD_quant_stop=10.026436;Kurtosis_quant_start=0.194552;Kurtosis_quant_stop=-1.846556;SVTYPE=INS;SUPTYPE=AL;SVLEN=12;STRANDS=+-;STRANDS2=20,15,20,15;RE=35;REF_strand=241290,243784;Strandbias_pval=0.402803;AF=7.21539e-05 GT:DR:DV 0/0:485039:35 +chr20 4685533 11 CACTGCACCTGGCTGTCAACATTCTTAAATCTCTTTCCTTACATGCTTCCTAAACCTCTCACCCAAAACTAGGAGACTAGATGTCCTATTT N . PASS IMPRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4685622;STD_quant_start=19.552493;STD_quant_stop=8.532292;Kurtosis_quant_start=0.223976;Kurtosis_quant_stop=2.098476;SVTYPE=DEL;SUPTYPE=AL;SVLEN=-89;STRANDS=+-;STRANDS2=5,6,5,6;RE=11;REF_strand=241299,244229;Strandbias_pval=1;AF=2.26557e-05 GT:DR:DV 0/0:485517:11 +chr20 4685507 12 N AAAAAAAAAAAAAAAAAAAAAAAA . PASS IMPRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4685535;STD_quant_start=10.170764;STD_quant_stop=10.941765;Kurtosis_quant_start=-1.987708;Kurtosis_quant_stop=-1.986335;SVTYPE=INS;SUPTYPE=AL;SVLEN=11;STRANDS=+-;STRANDS2=13,23,13,23;RE=36;REF_strand=241295,243980;Strandbias_pval=0.132698;AF=7.41847e-05 GT:DR:DV 0/0:485239:36 +chr20 4685661 13 AAAAGTGCCCAATTTGGGTAATAATTTATAAGATCCCCCTCCCTCTAAATCCTGTCCTTCTATCACTTCATCCTTCGCTCTCCTTTAAAATGAGACAGTTGTCAGCAGGAATCCTGCGCAAGAACACACCACCCTGTTTCATAGAAGA N . PASS IMPRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4685771;STD_quant_start=13.714955;STD_quant_stop=7.848567;Kurtosis_quant_start=-0.457595;Kurtosis_quant_stop=0.428424;SVTYPE=DEL;SUPTYPE=AL,NR;SVLEN=-110;STRANDS=+-;STRANDS2=5,7,5,7;RE=12;REF_strand=241306,244888;Strandbias_pval=0.774485;AF=2.46815e-05 GT:DR:DV 0/0:486182:12 +chr20 4685671 14 ATTTGGGTAAT N . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4685683;STD_quant_start=3.554202;STD_quant_stop=3.539691;Kurtosis_quant_start=-1.414354;Kurtosis_quant_stop=-1.440197;SVTYPE=DEL;SUPTYPE=AL,NR;SVLEN=-12;STRANDS=+-;STRANDS2=78,58,78,58;RE=136;REF_strand=241306,244669;Strandbias_pval=0.0859266;AF=0.00027985 GT:DR:DV 0/0:485839:136 +chr20 4685702 15 N CCCCCCCCCCCCCCCCCT . STRANDBIAS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4685711;STD_quant_start=8.366600;STD_quant_stop=6.812618;Kurtosis_quant_start=-2.115762;Kurtosis_quant_stop=-1.706274;SVTYPE=INS;SUPTYPE=AL;SVLEN=11;STRANDS=+-;STRANDS2=9,26,9,26;RE=35;REF_strand=241306,244854;Strandbias_pval=0.00603235;AF=7.19928e-05 GT:DR:DV 0/0:486125:35 +chr20 4685693 16 ATCCCCCTCCCTCTAA N . STRANDBIAS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4685709;STD_quant_start=4.421915;STD_quant_stop=4.562894;Kurtosis_quant_start=-1.524667;Kurtosis_quant_stop=-1.232430;SVTYPE=DEL;SUPTYPE=AL;SVLEN=-16;STRANDS=+-;STRANDS2=121,179,121,179;RE=300;REF_strand=241306,244809;Strandbias_pval=0.0014504;AF=0.000617138 GT:DR:DV 0/0:485815:300 +chr20 4685835 17 N TTTTTTTTTTT . STRANDBIAS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4685842;STD_quant_start=2.703274;STD_quant_stop=6.158172;Kurtosis_quant_start=-1.573176;Kurtosis_quant_stop=-1.659534;SVTYPE=INS;SUPTYPE=AL;SVLEN=11;STRANDS=+-;STRANDS2=58,20,58,20;RE=78;REF_strand=241312,245488;Strandbias_pval=1.14995e-05;AF=0.00016023 GT:DR:DV 0/0:486722:78 +chr20 4685860 18 N TCTAACATATTATAAAAGTAGAAATAATG . STRANDBIAS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4685869;STD_quant_start=6.284903;STD_quant_stop=8.062258;Kurtosis_quant_start=0.389000;Kurtosis_quant_stop=-0.878223;SVTYPE=INS;SUPTYPE=AL;SVLEN=12;STRANDS=+-;STRANDS2=0,13,0,13;RE=13;REF_strand=241316,245621;Strandbias_pval=0.0002456;AF=2.66975e-05 GT:DR:DV 0/0:486924:13 +chr20 4685896 19 N GTCAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA . PASS IMPRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4685941;STD_quant_start=16.721244;STD_quant_stop=13.472194;Kurtosis_quant_start=-2.004261;Kurtosis_quant_stop=-2.066924;SVTYPE=INS;SUPTYPE=AL;SVLEN=11;STRANDS=+-;STRANDS2=23,38,23,38;RE=61;REF_strand=241320,245870;Strandbias_pval=0.07292;AF=0.000125208 GT:DR:DV 0/0:487129:61 +chr20 4685956 20 GCCTCAAAATTTAAGAGTTTATGTGA N . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4685982;STD_quant_start=2.258318;STD_quant_stop=6.877500;Kurtosis_quant_start=-0.331319;Kurtosis_quant_stop=-1.582529;SVTYPE=DEL;SUPTYPE=AL;SVLEN=-26;STRANDS=+-;STRANDS2=12,9,12,9;RE=21;REF_strand=241261,246090;Strandbias_pval=0.51971;AF=4.30901e-05 GT:DR:DV 0/0:487330:21 +chr20 4686021 21 N TTTTTTTTTTTTTTTT . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4686029;STD_quant_start=7.002232;STD_quant_stop=7.371821;Kurtosis_quant_start=-1.786371;Kurtosis_quant_stop=-1.749839;SVTYPE=INS;SUPTYPE=AL;SVLEN=11;STRANDS=+-;STRANDS2=40,25,40,25;RE=65;REF_strand=240959,246316;Strandbias_pval=0.062113;AF=0.000133395 GT:DR:DV 0/0:487210:65 +chr20 4686016 22 TTTTTTGCTCTCCTCTTTAGAAATTTCTGGTTGCCAAAGTTCCAGAAATTGCTTCCT N . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4686076;STD_quant_start=4.615192;STD_quant_stop=9.332738;Kurtosis_quant_start=-0.793269;Kurtosis_quant_stop=0.641168;SVTYPE=DEL;SUPTYPE=AL;SVLEN=-60;STRANDS=+-;STRANDS2=7,10,7,10;RE=17;REF_strand=240852,246458;Strandbias_pval=0.629446;AF=3.48854e-05 GT:DR:DV 0/0:487293:17 +chr20 4686075 23 CCTCATTCCTGAG N . STRANDBIAS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4686088;STD_quant_start=5.003152;STD_quant_stop=5.524312;Kurtosis_quant_start=-1.680162;Kurtosis_quant_stop=-1.654740;SVTYPE=DEL;SUPTYPE=AL,NR;SVLEN=-13;STRANDS=+-;STRANDS2=279,167,280,166;RE=445;REF_strand=240671,246647;Strandbias_pval=2.5336e-08;AF=0.000913161 GT:DR:DV 0/0:486873:445 +chr20 4686079 24 N TTCTCTTGGGTG . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4686086;STD_quant_start=5.009990;STD_quant_stop=4.658326;Kurtosis_quant_start=-2.031605;Kurtosis_quant_stop=-2.090134;SVTYPE=INS;SUPTYPE=AL;SVLEN=12;STRANDS=+-;STRANDS2=12,7,12,7;RE=19;REF_strand=240665,246654;Strandbias_pval=0.257923;AF=3.89888e-05 GT:DR:DV 0/0:487300:19 +chr20 4686066 25 GTTCCAGAAATTGCTTCCTCATTCCTGAGCCTTTCATTTTCTCGATTTCTCCATTATGTAACGGGGAGCTGGAGCTTTGGGCCGAATTTCC N . PASS IMPRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4686158;STD_quant_start=12.083046;STD_quant_stop=18.697593;Kurtosis_quant_start=-1.186405;Kurtosis_quant_stop=0.653408;SVTYPE=DEL;SUPTYPE=AL;SVLEN=-92;STRANDS=+-;STRANDS2=7,4,7,4;RE=11;REF_strand=240543,246780;Strandbias_pval=0.381906;AF=2.25723e-05 GT:DR:DV 0/0:487312:11 +chr20 4686094 26 ATTTTCTCGATTTCTCCATTATGTAACGGGGAGCTGGAGCTTTGGGCCGAATTTCCAATTAAAGATGATTTTTACAGTCAATGAGCCACGTCAGGGAGCGATGGCACCCGCAGGCGGTATCAACTGATGCAAGTGTTCAAGCGAATCTCAACTCGTTTTTTCCGGTGACTCATTCCCGGCCCT N . PASS IMPRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4686284;STD_quant_start=16.398171;STD_quant_stop=19.922349;Kurtosis_quant_start=-1.087795;Kurtosis_quant_stop=-0.669784;SVTYPE=DEL;SUPTYPE=AL;SVLEN=-190;STRANDS=+-;STRANDS2=6,5,6,5;RE=11;REF_strand=240104,247118;Strandbias_pval=0.771402;AF=2.2577e-05 GT:DR:DV 0/0:487211:11 +chr20 4686134 27 N TTTTTTTTTTTTTTTTTTTTTTTTTT . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4686145;STD_quant_start=6.925065;STD_quant_stop=6.265849;Kurtosis_quant_start=-1.713714;Kurtosis_quant_stop=-1.449399;SVTYPE=INS;SUPTYPE=AL;SVLEN=11;STRANDS=+-;STRANDS2=27,19,27,19;RE=46;REF_strand=240420,246923;Strandbias_pval=0.238543;AF=9.43894e-05 GT:DR:DV 0/0:487297:46 +chr20 4686169 28 AGCCACGTCAGGGAGCGATGGCACCCGCAGGCGGTATCAACTGATGCAAGTGTTCAAGCGAATCTCAACTCGTTTTTTCCGGTGACTCATTCCCGGCCCTGC N . PASS IMPRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4686279;STD_quant_start=18.584940;STD_quant_stop=27.806474;Kurtosis_quant_start=0.131817;Kurtosis_quant_stop=-0.456090;SVTYPE=DEL;SUPTYPE=AL;SVLEN=-110;STRANDS=+-;STRANDS2=5,5,5,5;RE=10;REF_strand=239934,247286;Strandbias_pval=1;AF=2.05246e-05 GT:DR:DV 0/0:487210:10 +chr20 4686162 29 N TTTTTTTTTTTTTTTTTTTGTTTTTTTTTTTTTTTTTT . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4686184;STD_quant_start=2.937955;STD_quant_stop=8.958971;Kurtosis_quant_start=-1.490589;Kurtosis_quant_stop=-1.965134;SVTYPE=INS;SUPTYPE=AL;SVLEN=11;STRANDS=+-;STRANDS2=26,12,26,12;RE=38;REF_strand=240243,247075;Strandbias_pval=0.0222631;AF=7.79778e-05 GT:DR:DV 0/0:487280:38 +chr20 4686249 30 N TTTTTCTCTCTCTCTCTTTT . STRANDBIAS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4686250;STD_quant_start=2.463060;STD_quant_stop=6.005553;Kurtosis_quant_start=-1.353237;Kurtosis_quant_stop=-1.590623;SVTYPE=INS;SUPTYPE=AL;SVLEN=12;STRANDS=+-;STRANDS2=42,18,42,18;RE=60;REF_strand=239824,247402;Strandbias_pval=0.00170129;AF=0.000123146 GT:DR:DV 0/0:487166:60 +chr20 4686246 31 GTTTTTTCCGGTGACTCATTCCCGGCCCTGCTTGGCAGCGCTGCACCCTTTAACTT N . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4686306;STD_quant_start=4.098780;STD_quant_stop=9.929753;Kurtosis_quant_start=-1.167183;Kurtosis_quant_stop=-0.325546;SVTYPE=DEL;SUPTYPE=AL,NR;SVLEN=-60;STRANDS=+-;STRANDS2=5,12,5,12;RE=17;REF_strand=239665,247500;Strandbias_pval=0.144337;AF=3.48958e-05 GT:DR:DV 0/0:487148:17 +chr20 4686280 32 CTTGGCAGCGCTGCACCCTTTAACTTAAACCTCGGCCGGCCGCCCGCCGGGGGCACAGAGTGTGCGCCGGGCCGCGCGGCAATTGGTCCCCGCGCCGACCTCCGCCCGCGAGCGCCGCCGCTTCCCTTCCCCGCCCCGCGTCCCTCCCCCTCGGCCCCGCGCGTCGCCTGTCCTCCGAGCCAGTCGCTGACAGCCGCGGCGCCGCGAGC N . PASS IMPRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4686488;STD_quant_start=20.107213;STD_quant_stop=26.117044;Kurtosis_quant_start=-1.047828;Kurtosis_quant_stop=-1.499180;SVTYPE=DEL;SUPTYPE=AL;SVLEN=-208;STRANDS=+-;STRANDS2=8,4,8,4;RE=12;REF_strand=238945,248040;Strandbias_pval=0.258752;AF=2.46414e-05 GT:DR:DV 0/0:486973:12 +chr20 4686310 33 GCCCGCCGGGGG N . STRANDBIAS IMPRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4686341;STD_quant_start=8.051292;STD_quant_stop=10.232632;Kurtosis_quant_start=-1.890632;Kurtosis_quant_stop=-1.777171;SVTYPE=DEL;SUPTYPE=AL,NR;SVLEN=-31;STRANDS=+-;STRANDS2=201,332,201,332;RE=533;REF_strand=239326,247709;Strandbias_pval=1.38873e-07;AF=0.00109438 GT:DR:DV 0/0:486502:533 +chr20 4686307 34 N AGAGAGAAGAGG . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4686315;STD_quant_start=6.645801;STD_quant_stop=2.309401;Kurtosis_quant_start=-1.447947;Kurtosis_quant_stop=-0.405846;SVTYPE=INS;SUPTYPE=AL;SVLEN=11;STRANDS=+-;STRANDS2=11,13,11,13;RE=24;REF_strand=239423,247643;Strandbias_pval=0.839366;AF=4.92746e-05 GT:DR:DV 0/0:487042:24 +chr20 4686326 35 GGGGGCACAGAGTGTGCGCCGGGCCGCGCGGCAATTGGTCCCCGCGCCGACCTCCGCCCGCGAGCGCCGCCGCTTCCCTTCCCCGCCCCGCGTCCCTCCCCCTCGGCCCCGCGCGTCGCCTGTCCTCCGAGCCAGTCGCTGACAGCCGCGGCGCCGCGAGCTTCTCCTCTCCTCACGACCGAGGCAGGTAAACGCCCGGGGTGGGAGGAACGCGGGCGGGGGCAGGGGAGCCGCGGGGGCCGAGTGAGGACCCCGGGCCTCGGGTCCCAGGCGCAAGGGTGCCCGGCCGGGCGGGGTCGGGACCCCAGTGAGGAGGGGCCGGGGGCTGCCCCGCGGGCGCGTGACGCGTCTCGGGCCTGCCCGGCTGCGCTGGTCTCCGCTCGGGTGAGGCGGCTTGGCTTCGCTTTTCAGGTTAGGAAAGCTCCCTTTACTGCGCGTTGGGGGGCTGGGGGAGCTGGCGGAGCCCCGTTAGGGAGGTCGGTGGCGCCGGGGTGTCTCAGCGCCCCCTGCACCCCGCGCGGGTCCGGCCCAGCGGGCGATCGCTGGCGCCCAGGGAACTCCGGGAGGGCCGCCAGCGGGCTCCGCAGGGCGCGGGGCGGGGAGGGGCGCCTGGGGGCCGCGGGGCTCGCGCTCCCCGCCCGTTGGCCGCCCCTCGGAGGCCGAGATCGGGGCCCAGAACGCCCCTTGGCAAGGCCTGGCGCTTCCGCGATGCCCAGAGGGTGCTTGGGGGGATGGAGAGAGGGGCGCCCGCCG N . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4687079;STD_quant_start=0.000000;STD_quant_stop=0.000000;Kurtosis_quant_start=-1.183341;Kurtosis_quant_stop=-0.164071;SVTYPE=DEL;SUPTYPE=AL;SVLEN=-753;STRANDS=+-;STRANDS2=9,11,9,11;RE=20;REF_strand=236969,249618;Strandbias_pval=0.824987;AF=4.11026e-05 GT:DR:DV 0/0:486567:20 +chr20 4686320 36 GGCACAGAGTGTGCGCCGGGCCGCGCGGCAATTGGTCCCCGCGCCGACCTCCGCCCGCGAGCGCCGCCGCTTCCCTTCCCCGCCC N . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4686395;STD_quant_start=5.916080;STD_quant_stop=8.797727;Kurtosis_quant_start=-1.787833;Kurtosis_quant_stop=-1.889161;SVTYPE=DEL;SUPTYPE=AL,NR;SVLEN=-75;STRANDS=+-;STRANDS2=6,12,6,12;RE=18;REF_strand=239089,247845;Strandbias_pval=0.239251;AF=3.6966e-05 GT:DR:DV 0/0:486916:18 +chr20 4686366 37 N CCGCGCCGACCACGCACCT . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4686374;STD_quant_start=9.831184;STD_quant_stop=9.076966;Kurtosis_quant_start=-1.993439;Kurtosis_quant_stop=-1.941752;SVTYPE=INS;SUPTYPE=AL;SVLEN=11;STRANDS=+-;STRANDS2=28,18,28,18;RE=46;REF_strand=239001,247902;Strandbias_pval=0.139549;AF=9.44747e-05 GT:DR:DV 0/0:486857:46 +chr20 4686449 38 CCTCCGAGCCAGTCGCTGACAGCCGCGGCGCCGCGAGCTTCTCCTCTCCTCACGACCGAG N . PASS IMPRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4686524;STD_quant_start=4.207137;STD_quant_stop=14.949916;Kurtosis_quant_start=-1.853184;Kurtosis_quant_stop=-2.324605;SVTYPE=DEL;SUPTYPE=AL;SVLEN=-75;STRANDS=+-;STRANDS2=11,9,11,9;RE=20;REF_strand=238291,248541;Strandbias_pval=0.658247;AF=4.10819e-05 GT:DR:DV 0/0:486812:20 +chr20 4686482 39 CGAGCTTCTCCTCTCCTCACGACCGAGGCAGGTAAACGCCCGGGGTGGGAGGAACGCGGGCGGGGGCAGGGGAGCCGCGGGGGCCGAGTGAGGACCCCGGGCCTCGGGTCCCAGGCGCAAGGGTGCCC N . PASS IMPRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4686626;STD_quant_start=7.842194;STD_quant_stop=17.093859;Kurtosis_quant_start=-0.454638;Kurtosis_quant_stop=-1.319397;SVTYPE=DEL;SUPTYPE=AL;SVLEN=-144;STRANDS=+-;STRANDS2=4,9,4,9;RE=13;REF_strand=237893,248926;Strandbias_pval=0.268453;AF=2.6704e-05 GT:DR:DV 0/0:486806:13 +chr20 4686506 40 N GGTTGCAAGTG . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4686510;STD_quant_start=3.741657;STD_quant_stop=6.595453;Kurtosis_quant_start=-1.245641;Kurtosis_quant_stop=-1.714585;SVTYPE=INS;SUPTYPE=AL;SVLEN=11;STRANDS=+-;STRANDS2=12,6,12,6;RE=18;REF_strand=238172,248669;Strandbias_pval=0.159593;AF=3.69731e-05 GT:DR:DV 0/0:486823:18 +chr20 4686543 41 GGGGGCAGGGGAGCCGCGGGGGCCGAGTGAGGACCCCGGGCCTCGGGTCCCAGGCGCAAGGGTGCCCGGCCGGGCGGGGTCGGGACCCCAGTGAGGAGGGGCCGGGGGCTGCCCCGCGGGCGCGTGACGCGTCTCGGGCCTGCCCGGCTGCGCTGGTCTCCGCTCGGGTGAGGCGGCTTGGCTTCGCTTTTCAGGTTAGGAAAGCTCCCTTTACTGCGCGTTGGGGGGCTGGGGGAGCTGGCGGAGCCCCGTTAGGGAGGTCGGTGGCGCCGGGGTGTCTCAGCGCCCCCTGCACCCCGCGCGGGTCCGGCCCAGCGGGCGATCGCTGGCGCCCAGGGAACTCCGGGAGGGCCGCCAGCGGGCTCCGCAGGGCGCGGGGCGGGGAGGGGCGCCTGGGGGCCGCGGGGCTCGCGCTCCCCGCCCGTTGGCCGCCCCTCGGAGGCCGAGATCGGGGCCCAGAACGCCCCTTGGCAAGGCCTGGCGCTTCCGCGATGCCCAGAGGGTGCTTGGGGGGATGGAGAGAGGGGCGCCCGCCGGGGGAGTTCCGGGAGCCTCGGTGCCTCCCGCCGCAGCTGCAGCGTTCCTCCCGGGAGGCGGCCCAGCCCTTCATCCTCGCCGCCTGAGCTTCTCCGAGGGGGGCTGCAGCCTTGCGGCCGTTGCCACCGCCTGGAGAAGCGGCCCACGCGGACTGACGGGCG N . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4687238;STD_quant_start=2.828427;STD_quant_stop=2.509980;Kurtosis_quant_start=0.522505;Kurtosis_quant_stop=2.781087;SVTYPE=DEL;SUPTYPE=AL;SVLEN=-695;STRANDS=+-;STRANDS2=8,7,8,7;RE=15;REF_strand=235820,250320;Strandbias_pval=0.799015;AF=3.08553e-05 GT:DR:DV 0/0:486125:15 +chr20 4686543 42 N CTGTGCCGGCCGGCCACGCTGTCAT . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4686552;STD_quant_start=6.485882;STD_quant_stop=5.416026;Kurtosis_quant_start=-2.206242;Kurtosis_quant_stop=-0.680445;SVTYPE=INS;SUPTYPE=AL;SVLEN=11;STRANDS=+-;STRANDS2=21,10,21,10;RE=31;REF_strand=237823,248822;Strandbias_pval=0.0466925;AF=6.37015e-05 GT:DR:DV 0/0:486614:31 +chr20 4686554 43 AGCCGCGGGGGCCGAGTGAGGACCCCGGGCCTCGGGTCCCAGGCGCAAGGGTGCCCGGCCGGGCGGGGTCGGGACCCCAGTGAGGAGGGGCCGGGGGC N . PASS IMPRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4686653;STD_quant_start=10.421132;STD_quant_stop=11.895377;Kurtosis_quant_start=-0.753286;Kurtosis_quant_stop=-1.535989;SVTYPE=DEL;SUPTYPE=AL;SVLEN=-99;STRANDS=+-;STRANDS2=5,8,5,8;RE=13;REF_strand=237579,249169;Strandbias_pval=0.582473;AF=2.67079e-05 GT:DR:DV 0/0:486735:13 +chr20 4686565 44 CCGAGTGAGGACCCCGGGCCTCGGGT N . STRANDBIAS IMPRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4686595;STD_quant_start=6.257086;STD_quant_stop=10.300158;Kurtosis_quant_start=-1.544636;Kurtosis_quant_stop=-1.730958;SVTYPE=DEL;SUPTYPE=AL,NR;SVLEN=-30;STRANDS=+-;STRANDS2=497,126,497,126;RE=623;REF_strand=237651,249013;Strandbias_pval=5.47382e-57;AF=0.00128014 GT:DR:DV 0/0:486041:623 +chr20 4686612 45 GGGCGGGGTCGGGACCCCAGTGAGGAGGGGCCGGGGGCTGCCCCGCGGGCGCGT N . PASS IMPRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4686696;STD_quant_start=7.637626;STD_quant_stop=10.551461;Kurtosis_quant_start=-1.659967;Kurtosis_quant_stop=-1.791084;SVTYPE=DEL;SUPTYPE=AL;SVLEN=-84;STRANDS=+-;STRANDS2=12,12,12,12;RE=24;REF_strand=237332,249447;Strandbias_pval=1;AF=4.93037e-05 GT:DR:DV 0/0:486755:24 +chr20 4686637 46 GAGGGGCCGGGGGCT N . STRANDBIAS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4686653;STD_quant_start=3.612685;STD_quant_stop=4.385552;Kurtosis_quant_start=-1.272466;Kurtosis_quant_stop=-0.653821;SVTYPE=DEL;SUPTYPE=AL;SVLEN=-16;STRANDS=+-;STRANDS2=266,472,266,472;RE=738;REF_strand=237392,249437;Strandbias_pval=4.27533e-12;AF=0.00151593 GT:DR:DV 0/0:486091:738 +chr20 4686698 47 CCGCGGGCGCGTGACGCGTCTCGGGCCTGCCCGGCTGCGCTGGTCTCCGCTCGGGTGAGGCGGCTTGGCTTCGCTTTTCAGGTTAGGAAAGCTCCCTTTACTGCGCGTTGGGGGGCTGGGGGAGCTGGCGGAGCCCCGTTAGGGAGGT N . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4686804;STD_quant_start=7.829432;STD_quant_stop=5.089204;Kurtosis_quant_start=-1.541046;Kurtosis_quant_stop=-0.880568;SVTYPE=DEL;SUPTYPE=AL;SVLEN=-106;STRANDS=+-;STRANDS2=6,11,6,11;RE=17;REF_strand=236808,249923;Strandbias_pval=0.33531;AF=3.49269e-05 GT:DR:DV 0/0:486714:17 +chr20 4686712 48 N GCAGCGACAGGGACAGGCAGGCGGAGCC . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4686723;STD_quant_start=3.098387;STD_quant_stop=3.146427;Kurtosis_quant_start=-1.624389;Kurtosis_quant_stop=-1.337512;SVTYPE=INS;SUPTYPE=AL;SVLEN=11;STRANDS=+-;STRANDS2=8,12,8,12;RE=20;REF_strand=236977,249771;Strandbias_pval=0.506418;AF=4.1089e-05 GT:DR:DV 0/0:486728:20 +chr20 4686742 49 N CCCTCTCTCTCTCTCTCTCTCT . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4686755;STD_quant_start=5.468089;STD_quant_stop=7.211103;Kurtosis_quant_start=-1.821794;Kurtosis_quant_stop=-1.262056;SVTYPE=INS;SUPTYPE=AL;SVLEN=13;STRANDS=+-;STRANDS2=12,4,12,4;RE=16;REF_strand=236808,249906;Strandbias_pval=0.0442569;AF=3.28735e-05 GT:DR:DV 0/0:486698:16 +chr20 4686796 50 N GGCGGCGTTGGCTGACC . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4686805;STD_quant_start=6.177918;STD_quant_stop=4.898979;Kurtosis_quant_start=-1.794209;Kurtosis_quant_stop=-1.733320;SVTYPE=INS;SUPTYPE=AL;SVLEN=11;STRANDS=+-;STRANDS2=11,14,11,14;RE=25;REF_strand=236530,250131;Strandbias_pval=0.692924;AF=5.13705e-05 GT:DR:DV 0/0:486636:25 +chr20 4686807 51 CGGGGTGTCTCAGCGCCCCCTGCACCCCGCGCGGGTCCGGCCCAGCGGGCGATCGCTGGCGCCCAGGGAACTCCGGGAGGGCCGCCAGCGGGCTCCGCAGGGCGCGGGGCGGGGAGGGGCGCCTGGGGGCCGCGGGGCTCGCGCTCCCCGCCCGTTGGCCGCCCCT N . PASS IMPRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4686971;STD_quant_start=14.166863;STD_quant_stop=21.071308;Kurtosis_quant_start=-0.439120;Kurtosis_quant_stop=-1.304334;SVTYPE=DEL;SUPTYPE=AL,NR;SVLEN=-164;STRANDS=+-;STRANDS2=7,5,7,5;RE=12;REF_strand=235881,250557;Strandbias_pval=0.571369;AF=2.46691e-05 GT:DR:DV 0/0:486426:12 +chr20 4686831 52 CCCCTGCACCCCG N . STRANDBIAS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4686842;STD_quant_start=2.829455;STD_quant_stop=3.763348;Kurtosis_quant_start=-0.271513;Kurtosis_quant_stop=-0.139149;SVTYPE=DEL;SUPTYPE=AL,NR;SVLEN=-11;STRANDS=+-;STRANDS2=214,131,214,131;RE=345;REF_strand=236281,250272;Strandbias_pval=6.19918e-07;AF=0.00070907 GT:DR:DV 0/0:486208:345 +chr20 4686855 53 N CTGCCCACGCTTCTAGCGCGTG . PASS IMPRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4686865;STD_quant_start=10.221360;STD_quant_stop=10.162958;Kurtosis_quant_start=-2.086662;Kurtosis_quant_stop=-2.003463;SVTYPE=INS;SUPTYPE=AL;SVLEN=11;STRANDS=+-;STRANDS2=18,25,18,25;RE=43;REF_strand=236144,250388;Strandbias_pval=0.446367;AF=8.83806e-05 GT:DR:DV 0/0:486489:43 +chr20 4686928 54 GGGGCGCCTGGG N . STRANDBIAS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4686944;STD_quant_start=8.504728;STD_quant_stop=8.358825;Kurtosis_quant_start=-1.665980;Kurtosis_quant_stop=-1.639106;SVTYPE=DEL;SUPTYPE=AL,NR;SVLEN=-16;STRANDS=+-;STRANDS2=333,805,333,805;RE=1138;REF_strand=235559,250731;Strandbias_pval=1.92615e-39;AF=0.00234017 GT:DR:DV 0/0:485152:1138 +chr20 4686913 55 GCTCCGCAGGGCGCGGGGCGGGGAGGGGCGCCTGGGGGCCGCGGGGCTCGCGCTCCCCGCCCGTTGGCCGCCCCTCGGAGGCCGAGATCGGGGCCCAGAACGCCCCT N . PASS IMPRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4687011;STD_quant_start=17.083130;STD_quant_stop=4.582576;Kurtosis_quant_start=-2.238019;Kurtosis_quant_stop=-1.623246;SVTYPE=DEL;SUPTYPE=AL;SVLEN=-98;STRANDS=+-;STRANDS2=14,10,14,10;RE=24;REF_strand=235372,250892;Strandbias_pval=0.415013;AF=4.93559e-05 GT:DR:DV 0/0:486240:24 +chr20 4686914 56 GGGCGCGGGGCGGGGAGGGGCGCCTGGGGGCCGCGGGGCTCGCGCTCCCCGCCCGTTGGCCGCCCCTCGGAGGCCGAGATCGGGGCCCAGAACGCCCCTTGGCAAGGCCTGGCGCTTCCGCGATGCCCAGAGGGTGCTTGGGGGGATGGAGAGAGG N . PASS IMPRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4687072;STD_quant_start=23.515952;STD_quant_stop=31.351236;Kurtosis_quant_start=-1.191913;Kurtosis_quant_stop=-0.374136;SVTYPE=DEL;SUPTYPE=AL,NR;SVLEN=-158;STRANDS=+-;STRANDS2=9,2,9,2;RE=11;REF_strand=235216,251057;Strandbias_pval=0.0334297;AF=2.2621e-05 GT:DR:DV 0/0:486262:11 +chr20 4686937 57 GGGGGCCGCGGGGCTCGCGCTCCCCGCCC N . STRANDBIAS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4686971;STD_quant_start=5.962848;STD_quant_stop=5.491857;Kurtosis_quant_start=-1.929757;Kurtosis_quant_stop=-1.897565;SVTYPE=DEL;SUPTYPE=AL;SVLEN=-34;STRANDS=+-;STRANDS2=270,217,270,217;RE=487;REF_strand=235407,250843;Strandbias_pval=0.00201841;AF=0.00100154 GT:DR:DV 0/0:485763:487 +chr20 4687009 58 N GCGCGCCACGCCTT . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4687013;STD_quant_start=8.081317;STD_quant_stop=8.561991;Kurtosis_quant_start=-1.774263;Kurtosis_quant_stop=-1.605280;SVTYPE=INS;SUPTYPE=AL;SVLEN=11;STRANDS=+-;STRANDS2=14,12,14,12;RE=26;REF_strand=235044,251166;Strandbias_pval=0.695614;AF=5.34748e-05 GT:DR:DV 0/0:486184:26 +chr20 4687019 59 GGCGCTTCCGCGATGCCCAGAGGGTGCTTGGGGGGATGGAGAGAGGGGCGCCCGCCGGGGGAGTTCCGGGAGCCTCGGTGCCTCCCGCCGCAGCTGCAGCGTTCCTCCCG N . PASS IMPRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4687142;STD_quant_start=14.791890;STD_quant_stop=18.002778;Kurtosis_quant_start=-1.165058;Kurtosis_quant_stop=-1.175801;SVTYPE=DEL;SUPTYPE=AL;SVLEN=-123;STRANDS=+-;STRANDS2=4,9,4,9;RE=13;REF_strand=234670,251527;Strandbias_pval=0.270612;AF=2.67381e-05 GT:DR:DV 0/0:486184:13 +chr20 4687064 60 GGGGGGATGGAGAGAGGGGCGCCCGCC N . STRANDBIAS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4687078;STD_quant_start=1.446526;STD_quant_stop=1.680336;Kurtosis_quant_start=0.109723;Kurtosis_quant_stop=1.810835;SVTYPE=DEL;SUPTYPE=AL;SVLEN=-14;STRANDS=+-;STRANDS2=47,191,47,191;RE=238;REF_strand=234704,251489;Strandbias_pval=9.72608e-20;AF=0.000489518 GT:DR:DV 0/0:485955:238 +chr20 4687051 61 N GGGGGGGGGGGG . STRANDBIAS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4687051;STD_quant_start=1.109400;STD_quant_stop=2.557042;Kurtosis_quant_start=-1.010384;Kurtosis_quant_stop=-1.140769;SVTYPE=INS;SUPTYPE=AL;SVLEN=15;STRANDS=+-;STRANDS2=21,6,21,6;RE=27;REF_strand=234846,251400;Strandbias_pval=0.00306546;AF=5.55274e-05 GT:DR:DV 0/0:486219:27 +chr20 4687100 62 N GAGGGGGGGGGGG . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4687115;STD_quant_start=5.838093;STD_quant_stop=7.461010;Kurtosis_quant_start=-0.366449;Kurtosis_quant_stop=0.167688;SVTYPE=INS;SUPTYPE=AL;SVLEN=11;STRANDS=+-;STRANDS2=13,11,13,11;RE=24;REF_strand=234523,251675;Strandbias_pval=0.683908;AF=4.93626e-05 GT:DR:DV 0/0:486174:24 +chr20 4687087 63 GGAGCCTCGGTGCCTCCCGCCGCAGCTGCAGCGTTCCTCCCGGGAGGCGGCCCAGCCCTTCATCCTCGCCGCCTGAGCTTCTCCGAGGGGGGCTGCAGCCTTGCGGCCGTTGCCACCGCCTGGAGAAGCGGCCCACGCGGACTGAC N . PASS IMPRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4687243;STD_quant_start=27.395255;STD_quant_stop=29.354727;Kurtosis_quant_start=-1.151337;Kurtosis_quant_stop=-0.398703;SVTYPE=DEL;SUPTYPE=AL;SVLEN=-156;STRANDS=+-;STRANDS2=6,4,6,4;RE=10;REF_strand=234182,251714;Strandbias_pval=0.536501;AF=2.05805e-05 GT:DR:DV 0/0:485886:10 +chr20 4687178 64 GGGGGGCTGCAGCCTTGCGGCCGTTGCCACCGCCTGGAGAAGCGGCCCACGCGGACTGACGGGCGGGGGCGGG N . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4687249;STD_quant_start=9.887832;STD_quant_stop=4.341216;Kurtosis_quant_start=-1.793022;Kurtosis_quant_stop=-1.659811;SVTYPE=DEL;SUPTYPE=AL;SVLEN=-71;STRANDS=+-;STRANDS2=16,11,16,11;RE=27;REF_strand=233917,251843;Strandbias_pval=0.255859;AF=5.5583e-05 GT:DR:DV 0/0:485733:27 +chr20 4687166 65 CTTCTCCGAGGGGGGCTGCAGCCTTGC N . STRANDBIAS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4687194;STD_quant_start=7.160529;STD_quant_stop=5.699807;Kurtosis_quant_start=-1.802907;Kurtosis_quant_stop=-1.212446;SVTYPE=DEL;SUPTYPE=AL,NR;SVLEN=-28;STRANDS=+-;STRANDS2=167,243,167,243;RE=410;REF_strand=234125,251843;Strandbias_pval=0.00254711;AF=0.000843677 GT:DR:DV 0/0:485558:410 +chr20 4687237 66 N AGCAGAGCGTGAAGGAGGAA . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4687246;STD_quant_start=8.798674;STD_quant_stop=9.473648;Kurtosis_quant_start=-1.860603;Kurtosis_quant_stop=-1.967103;SVTYPE=INS;SUPTYPE=AL;SVLEN=11;STRANDS=+-;STRANDS2=18,6,18,6;RE=24;REF_strand=233768,251844;Strandbias_pval=0.012533;AF=4.94222e-05 GT:DR:DV 0/0:485588:24 +chr20 4687255 67 GACGGGCGGGGGCGGGGCCTCGGGCCTCGGCGGGGGCGGGGTCCGGGGAGGCCCCACCCTCTGTTCTCCAGGGGCGGGGAGAGAGGAGCTGCAGGTCTGCGGCCTGGCCCCAGGTGCGATGGCGGACCCCAGCTTGGC N . PASS IMPRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4687372;STD_quant_start=19.697716;STD_quant_stop=13.461055;Kurtosis_quant_start=0.732482;Kurtosis_quant_stop=0.036672;SVTYPE=DEL;SUPTYPE=AL;SVLEN=-117;STRANDS=+-;STRANDS2=5,5,5,5;RE=10;REF_strand=233304,251843;Strandbias_pval=1;AF=2.06123e-05 GT:DR:DV 0/0:485137:10 +chr20 4687302 68 AGGGGCGGGGAGAGAG N . STRANDBIAS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4687320;STD_quant_start=6.505876;STD_quant_stop=4.407953;Kurtosis_quant_start=-1.819617;Kurtosis_quant_stop=-1.645380;SVTYPE=DEL;SUPTYPE=AL,NR;SVLEN=-18;STRANDS=+-;STRANDS2=160,226,160,226;RE=386;REF_strand=233258,251842;Strandbias_pval=0.00932329;AF=0.000795712 GT:DR:DV 0/0:484714:386 +chr20 4687343 69 CAGGTGCGATGG N . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4687355;STD_quant_start=4.350066;STD_quant_stop=1.808101;Kurtosis_quant_start=-0.934609;Kurtosis_quant_stop=-0.898176;SVTYPE=DEL;SUPTYPE=AL;SVLEN=-12;STRANDS=+-;STRANDS2=29,23,29,23;RE=52;REF_strand=233049,251842;Strandbias_pval=0.270955;AF=0.000107241 GT:DR:DV 0/0:484839:52 +chr20 4687345 70 GGTGCGATGGCGGACCCCAGCTTGGCCAGTCACATTCCTCCCAGTCCCCCTGGAGGGAGAACGCTGGCCATGGGGGGCTCCAAGGAACAACCAGCCTCGGATGACGACCCTTGGGTCACCGGTCTCCCCACCTGTGCGGCAGGCGCCTTCACGTTTCATTATTAAACAATGGGGAGAAATCCATGTTTACTGTCCTTTTTAAG N . PASS IMPRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4687561;STD_quant_start=24.851559;STD_quant_stop=22.498889;Kurtosis_quant_start=-1.392934;Kurtosis_quant_stop=-1.263813;SVTYPE=DEL;SUPTYPE=AL;SVLEN=-216;STRANDS=+-;STRANDS2=7,4,7,4;RE=11;REF_strand=232487,251840;Strandbias_pval=0.372339;AF=2.27119e-05 GT:DR:DV 0/0:484316:11 +chr20 4687400 71 GGAGAACGCTGGCC N . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4687415;STD_quant_start=1.541104;STD_quant_stop=1.854050;Kurtosis_quant_start=2.571331;Kurtosis_quant_stop=-0.215701;SVTYPE=DEL;SUPTYPE=AL;SVLEN=-15;STRANDS=+-;STRANDS2=20,12,20,12;RE=32;REF_strand=232748,251842;Strandbias_pval=0.112927;AF=6.60352e-05 GT:DR:DV 0/0:484558:32 +chr20 4687390 72 N CCCCCCCCCCCCCCCCCCC . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4687398;STD_quant_start=1.748015;STD_quant_stop=4.196559;Kurtosis_quant_start=-0.176363;Kurtosis_quant_stop=-0.603609;SVTYPE=INS;SUPTYPE=AL;SVLEN=11;STRANDS=+-;STRANDS2=17,19,17,19;RE=36;REF_strand=232824,251842;Strandbias_pval=1;AF=7.4278e-05 GT:DR:DV 0/0:484630:36 +chr20 4687446 73 CCGGTCTCCCCACCTGTGCGGCAGGCGCCTTCACGTTTCATTATTAAACAATGGGGAGAAATCCATGTTTACT N . PASS IMPRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4687532;STD_quant_start=16.754104;STD_quant_stop=16.831518;Kurtosis_quant_start=-0.823195;Kurtosis_quant_stop=0.339160;SVTYPE=DEL;SUPTYPE=AL;SVLEN=-86;STRANDS=+-;STRANDS2=7,3,7,3;RE=10;REF_strand=232292,251840;Strandbias_pval=0.21113;AF=2.06555e-05 GT:DR:DV 0/0:484122:10 +chr20 4687471 74 CCCCACCTGTGCGGCAGGCGCCTTCACGTTTCATTATTAAACAATGGGGAGAAATCCATGTTTACTGTCCTTTTTAAGGAATTTTTTGCTCTTCTCTTTGAGGTGGCTGTAGGAAATAGATTTTTTTTTTAACCTCGCAATTCCACCACGG N . PASS IMPRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4687626;STD_quant_start=28.259512;STD_quant_stop=32.482303;Kurtosis_quant_start=-0.888024;Kurtosis_quant_stop=-0.948753;SVTYPE=DEL;SUPTYPE=AL,NR;SVLEN=-155;STRANDS=+-;STRANDS2=7,3,7,3;RE=10;REF_strand=231970,251836;Strandbias_pval=0.21093;AF=2.06694e-05 GT:DR:DV 0/0:483796:10 +chr20 4687508 75 N AAAAAAAAAAAAA . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4687508;STD_quant_start=2.631174;STD_quant_stop=3.689903;Kurtosis_quant_start=-1.688136;Kurtosis_quant_stop=-1.671090;SVTYPE=INS;SUPTYPE=AL;SVLEN=11;STRANDS=+-;STRANDS2=10,17,10,17;RE=27;REF_strand=232174,251842;Strandbias_pval=0.335825;AF=5.57833e-05 GT:DR:DV 0/0:483989:27 +chr20 4687540 76 TTTTTAAGGAATTT N . STRANDBIAS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4687566;STD_quant_start=7.289973;STD_quant_stop=9.294902;Kurtosis_quant_start=-1.343243;Kurtosis_quant_stop=-1.853322;SVTYPE=DEL;SUPTYPE=AL,NR;SVLEN=-26;STRANDS=+-;STRANDS2=186,148,186,148;RE=334;REF_strand=231906,251838;Strandbias_pval=0.00513855;AF=0.000690448 GT:DR:DV 0/0:483410:334 +chr20 4687590 77 N TTTTTTTTTTTTTTT . STRANDBIAS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4687590;STD_quant_start=0.000000;STD_quant_stop=3.108262;Kurtosis_quant_start=-1.129026;Kurtosis_quant_stop=-1.302025;SVTYPE=INS;SUPTYPE=AL;SVLEN=11;STRANDS=+-;STRANDS2=108,17,108,17;RE=125;REF_strand=231680,251834;Strandbias_pval=2.50364e-19;AF=0.000258524 GT:DR:DV 0/0:483389:125 +chr20 4687566 78 TTTGAGGTGGCT N . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4687582;STD_quant_start=1.664101;STD_quant_stop=2.807956;Kurtosis_quant_start=1.356409;Kurtosis_quant_stop=0.233533;SVTYPE=DEL;SUPTYPE=AL;SVLEN=-16;STRANDS=+-;STRANDS2=17,35,17,35;RE=52;REF_strand=231786,251836;Strandbias_pval=0.0363418;AF=0.000107522 GT:DR:DV 0/0:483570:52 +chr20 4687590 79 N TTTTTTTTTTTTTT . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4687593;STD_quant_start=0.000000;STD_quant_stop=1.303840;Kurtosis_quant_start=0.727285;Kurtosis_quant_stop=0.054608;SVTYPE=INS;SUPTYPE=AL;SVLEN=11;STRANDS=+-;STRANDS2=12,5,12,5;RE=17;REF_strand=231671,251834;Strandbias_pval=0.0870655;AF=3.51599e-05 GT:DR:DV 0/0:483488:17 +chr20 4687624 80 N CCTTTCTCCTTCT . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4687631;STD_quant_start=4.701064;STD_quant_stop=5.504544;Kurtosis_quant_start=-1.200470;Kurtosis_quant_stop=-1.055470;SVTYPE=INS;SUPTYPE=AL;SVLEN=11;STRANDS=+-;STRANDS2=11,6,11,6;RE=17;REF_strand=231529,251830;Strandbias_pval=0.224831;AF=3.51705e-05 GT:DR:DV 0/0:483342:17 +chr20 4687679 81 TCACACAACACAGTGCAGTTTCACTGCTGTAATGATGAGGATCTTCATGGCCGCGTTATTTTCT N . PASS IMPRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4687739;STD_quant_start=7.726578;STD_quant_stop=13.023056;Kurtosis_quant_start=-1.567802;Kurtosis_quant_stop=-0.755719;SVTYPE=DEL;SUPTYPE=AL;SVLEN=-60;STRANDS=+-;STRANDS2=6,9,6,9;RE=15;REF_strand=231066,251827;Strandbias_pval=0.612288;AF=3.10628e-05 GT:DR:DV 0/0:482878:15 +chr20 4687660 82 N TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTG . PASS IMPRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4687689;STD_quant_start=7.598733;STD_quant_stop=12.205038;Kurtosis_quant_start=-1.528967;Kurtosis_quant_stop=-1.822100;SVTYPE=INS;SUPTYPE=AL;SVLEN=11;STRANDS=+-;STRANDS2=34,20,34,20;RE=54;REF_strand=231274,251828;Strandbias_pval=0.0291564;AF=0.000111778 GT:DR:DV 0/0:483048:54 +chr20 4687742 83 CGCGTTATTTTCTTGTTCTGAGAGCATCACGGTTTAATTAGCAGTTCCCCATATGATTTGAAGTGTTTCCCGT N . PASS IMPRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4687817;STD_quant_start=15.735311;STD_quant_stop=16.613248;Kurtosis_quant_start=-0.268890;Kurtosis_quant_stop=-0.984193;SVTYPE=DEL;SUPTYPE=AL;SVLEN=-75;STRANDS=+-;STRANDS2=6,5,6,5;RE=11;REF_strand=230653,251817;Strandbias_pval=0.766773;AF=2.27993e-05 GT:DR:DV 0/0:482459:11 +chr20 4687819 84 N AAAAAAAAAAAAAAC . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4687827;STD_quant_start=8.146388;STD_quant_stop=5.376717;Kurtosis_quant_start=-1.901615;Kurtosis_quant_stop=-1.606089;SVTYPE=INS;SUPTYPE=AL;SVLEN=11;STRANDS=+-;STRANDS2=13,9,13,9;RE=22;REF_strand=230402,251807;Strandbias_pval=0.296498;AF=4.56234e-05 GT:DR:DV 0/0:482187:22 +chr20 4688000 85 N . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4688012;STD_quant_start=4.027682;STD_quant_stop=3.731746;Kurtosis_quant_start=-1.237693;Kurtosis_quant_stop=-1.689448;SVTYPE=DEL;SUPTYPE=AL;SVLEN=-12;STRANDS=+-;STRANDS2=49,59,49,59;RE=108;REF_strand=228565,251425;Strandbias_pval=0.700191;AF=0.000225005 GT:DR:DV 0/0:479882:108 +chr20 4688011 86 N AAAAAAAAAAAA . STRANDBIAS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4688011;STD_quant_start=0.000000;STD_quant_stop=1.183216;Kurtosis_quant_start=0.340675;Kurtosis_quant_stop=-0.009614;SVTYPE=INS;SUPTYPE=AL;SVLEN=11;STRANDS=+-;STRANDS2=9,52,9,52;RE=61;REF_strand=228370,251306;Strandbias_pval=9.93811e-08;AF=0.000127169 GT:DR:DV 0/0:479615:61 diff --git a/SVs_sniffles/vcf/54968_bodySnif.vcf b/SVs_sniffles/vcf/54968_bodySnif.vcf new file mode 100644 index 0000000..e441396 --- /dev/null +++ b/SVs_sniffles/vcf/54968_bodySnif.vcf @@ -0,0 +1,37 @@ +##fileformat=VCFv4.1 +##source=Sniffles +##fileDate=20210810:56:10 AMef_minus +##contig= +##ALT= +##ALT= +##ALT= +##ALT= +##ALT= +##ALT= +##FILTER= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##FORMAT= +##FORMAT= +##FORMAT= +#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT bamfilt/54968_f.bam +chr20 4693324 0 N CTCTCTCTCTCTCTCTCTCTCTCTCTCCCCCCCCCCCCCCCCCCCCCCCCCCCCC . PASS IMPRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4693328;STD_quant_start=16.899704;STD_quant_stop=19.662146;Kurtosis_quant_start=1.130638;Kurtosis_quant_stop=-0.745837;SVTYPE=INS;SUPTYPE=AL;SVLEN=43;STRANDS=+-;STRANDS2=5,5,5,5;RE=10;REF_strand=10432,13552;Strandbias_pval=0.755341;AF=0.000416945 GT:DR:DV 0/0:23974:10 diff --git a/SVs_sniffles/vcf/54968_promoterSnif.vcf b/SVs_sniffles/vcf/54968_promoterSnif.vcf new file mode 100644 index 0000000..2c86f32 --- /dev/null +++ b/SVs_sniffles/vcf/54968_promoterSnif.vcf @@ -0,0 +1,97 @@ +##fileformat=VCFv4.1 +##source=Sniffles +##fileDate=20210811:37:59 AMef_minus +##contig= +##ALT= +##ALT= +##ALT= +##ALT= +##ALT= +##ALT= +##FILTER= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##FORMAT= +##FORMAT= +##FORMAT= +#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT promoterbamfilt/54968_f.bam +chr20 4685111 0 CCTGGCTTCTC N . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4685122;STD_quant_start=4.021680;STD_quant_stop=4.629771;Kurtosis_quant_start=-1.534992;Kurtosis_quant_stop=-1.177683;SVTYPE=DEL;SUPTYPE=AL;SVLEN=-11;STRANDS=+-;STRANDS2=85,7,85,7;RE=92;REF_strand=198169,16885;Strandbias_pval=1;AF=0.0004278 GT:DR:DV 0/0:214962:92 +chr20 4685121 1 CCTGTCTCTCGCC N . PASS IMPRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4685155;STD_quant_start=10.448632;STD_quant_stop=6.735693;Kurtosis_quant_start=-1.832979;Kurtosis_quant_stop=-1.682438;SVTYPE=DEL;SUPTYPE=AL;SVLEN=-34;STRANDS=+-;STRANDS2=80,12,80,12;RE=92;REF_strand=198237,16916;Strandbias_pval=0.0778239;AF=0.000427603 GT:DR:DV 0/0:215061:92 +chr20 4685224 2 TTTTTTTTTTT N . STRANDBIAS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4685235;STD_quant_start=0.000000;STD_quant_stop=1.095078;Kurtosis_quant_start=1.567683;Kurtosis_quant_stop=1.321006;SVTYPE=DEL;SUPTYPE=AL,NR;SVLEN=-11;STRANDS=+-;STRANDS2=837,158,837,158;RE=995;REF_strand=198352,17001;Strandbias_pval=9.69918e-17;AF=0.00462032 GT:DR:DV 0/0:214358:995 +chr20 4685224 3 N TTTTTTTTTTT . STRANDBIAS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4685224;STD_quant_start=0.000000;STD_quant_stop=1.192436;Kurtosis_quant_start=40.489088;Kurtosis_quant_stop=1.482474;SVTYPE=INS;SUPTYPE=AL;SVLEN=11;STRANDS=+-;STRANDS2=6280,20,6280,20;RE=6300;REF_strand=198350,16994;Strandbias_pval=5.97794e-186;AF=0.0292555 GT:DR:DV 0/0:209044:6300 +chr20 4685224 4 AAGAGACAAAGAGTGAGACAGGGTCTTGGCC N . STRANDBIAS IMPRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4685274;STD_quant_start=14.787085;STD_quant_stop=4.062019;Kurtosis_quant_start=-2.101598;Kurtosis_quant_stop=-0.168235;SVTYPE=DEL;SUPTYPE=AL,NR;SVLEN=-50;STRANDS=+-;STRANDS2=57,19,57,19;RE=76;REF_strand=198364,17010;Strandbias_pval=5.25083e-06;AF=0.000352875 GT:DR:DV 0/0:215298:76 +chr20 4685315 5 AAGCTCACTGC N . STRANDBIAS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4685326;STD_quant_start=4.163332;STD_quant_stop=4.807800;Kurtosis_quant_start=-1.368042;Kurtosis_quant_stop=-1.344963;SVTYPE=DEL;SUPTYPE=AL;SVLEN=-11;STRANDS=+-;STRANDS2=150,24,150,24;RE=174;REF_strand=198570,17061;Strandbias_pval=0.00714882;AF=0.000806934 GT:DR:DV 0/0:215457:174 +chr20 4685349 6 AAGCAATCCTCCCAT N . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4685361;STD_quant_start=5.069965;STD_quant_stop=2.153222;Kurtosis_quant_start=-0.866063;Kurtosis_quant_stop=1.913139;SVTYPE=DEL;SUPTYPE=AL,NR;SVLEN=-12;STRANDS=+-;STRANDS2=80,9,80,9;RE=89;REF_strand=198578,17076;Strandbias_pval=0.429331;AF=0.000412698 GT:DR:DV 0/0:215565:89 +chr20 4685361 7 N CCTGCCTGTCTCCTCCCAG . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4685368;STD_quant_start=6.397544;STD_quant_stop=7.250616;Kurtosis_quant_start=-1.800701;Kurtosis_quant_stop=-1.764358;SVTYPE=INS;SUPTYPE=AL;SVLEN=12;STRANDS=+-;STRANDS2=27,2,27,2;RE=29;REF_strand=198579,17084;Strandbias_pval=1;AF=0.000134469 GT:DR:DV 0/0:215634:29 +chr20 4685413 8 N TTTTTTTATTTTTTTTT . STRANDBIAS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4685414;STD_quant_start=0.000000;STD_quant_stop=4.901814;Kurtosis_quant_start=6.432312;Kurtosis_quant_stop=-0.459733;SVTYPE=INS;SUPTYPE=AL;SVLEN=11;STRANDS=+-;STRANDS2=211,5,211,5;RE=216;REF_strand=198580,17102;Strandbias_pval=0.000895152;AF=0.00100147 GT:DR:DV 0/0:215466:216 +chr20 4685526 9 ACAGGCCTGAGCCACTGCACCTG N . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4685544;STD_quant_start=7.774053;STD_quant_stop=6.116392;Kurtosis_quant_start=-1.788351;Kurtosis_quant_stop=-1.729511;SVTYPE=DEL;SUPTYPE=AL,NR;SVLEN=-18;STRANDS=+-;STRANDS2=138,19,138,19;RE=157;REF_strand=198588,17140;Strandbias_pval=0.0738432;AF=0.000727768 GT:DR:DV 0/0:215571:157 +chr20 4685563 10 CTCTTTCCTTACATGCTTCCTAAACCTCTC N . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4685591;STD_quant_start=6.300685;STD_quant_stop=6.195447;Kurtosis_quant_start=-1.321544;Kurtosis_quant_stop=-1.863583;SVTYPE=DEL;SUPTYPE=AL;SVLEN=-28;STRANDS=+-;STRANDS2=140,7,140,7;RE=147;REF_strand=198588,17156;Strandbias_pval=0.171086;AF=0.000681363 GT:DR:DV 0/0:215597:147 +chr20 4685636 11 GCCTGGTTTAC N . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4685647;STD_quant_start=5.968545;STD_quant_stop=5.772144;Kurtosis_quant_start=-1.554810;Kurtosis_quant_stop=-1.442179;SVTYPE=DEL;SUPTYPE=AL,NR;SVLEN=-11;STRANDS=+-;STRANDS2=151,19,151,19;RE=170;REF_strand=198590,17178;Strandbias_pval=0.119466;AF=0.000787883 GT:DR:DV 0/0:215598:170 +chr20 4685642 12 TGGTTTACGCCCATTTCACTTTAAAAGTGCCCAATT N . PASS IMPRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4685684;STD_quant_start=8.306624;STD_quant_stop=15.578832;Kurtosis_quant_start=0.759045;Kurtosis_quant_stop=-0.638553;SVTYPE=DEL;SUPTYPE=AL,NR;SVLEN=-42;STRANDS=+-;STRANDS2=10,2,10,2;RE=12;REF_strand=198590,17183;Strandbias_pval=0.247027;AF=5.5614e-05 GT:DR:DV 0/0:215761:12 +chr20 4685726 13 CTTCATCCTTCG N . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4685738;STD_quant_start=3.624628;STD_quant_stop=4.295146;Kurtosis_quant_start=0.366889;Kurtosis_quant_stop=-0.293658;SVTYPE=DEL;SUPTYPE=AL,NR;SVLEN=-12;STRANDS=+-;STRANDS2=51,8,51,8;RE=59;REF_strand=198592,17208;Strandbias_pval=0.14096;AF=0.000273401 GT:DR:DV 0/0:215741:59 +chr20 4685689 14 TCTAAATCCTG N . STRANDBIAS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4685715;STD_quant_start=4.956389;STD_quant_stop=6.832584;Kurtosis_quant_start=-1.732697;Kurtosis_quant_stop=-1.542948;SVTYPE=DEL;SUPTYPE=AL;SVLEN=-26;STRANDS=+-;STRANDS2=127,25,127,25;RE=152;REF_strand=198590,17197;Strandbias_pval=0.00047812;AF=0.000704398 GT:DR:DV 0/0:215635:152 +chr20 4685728 15 N TCACATACTTTGAATCTCCTATTGTTG . PASS IMPRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4685739;STD_quant_start=10.387492;STD_quant_stop=9.219544;Kurtosis_quant_start=-1.565990;Kurtosis_quant_stop=-1.799061;SVTYPE=INS;SUPTYPE=AL;SVLEN=11;STRANDS=+-;STRANDS2=17,1,17,1;RE=18;REF_strand=198592,17208;Strandbias_pval=1;AF=8.34106e-05 GT:DR:DV 0/0:215782:18 +chr20 4685777 16 CGCAAGAACACAC N . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4685790;STD_quant_start=4.329669;STD_quant_stop=5.056820;Kurtosis_quant_start=-1.612893;Kurtosis_quant_stop=-1.541470;SVTYPE=DEL;SUPTYPE=AL,NR;SVLEN=-13;STRANDS=+-;STRANDS2=108,18,108,18;RE=126;REF_strand=198594,17218;Strandbias_pval=0.0193825;AF=0.000583841 GT:DR:DV 0/0:215686:126 +chr20 4685835 17 N TTTTTTTTTTTTTTT . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4685844;STD_quant_start=0.000000;STD_quant_stop=4.690416;Kurtosis_quant_start=-0.387420;Kurtosis_quant_stop=-1.309010;SVTYPE=INS;SUPTYPE=AL;SVLEN=11;STRANDS=+-;STRANDS2=25,2,25,2;RE=27;REF_strand=198594,17236;Strandbias_pval=1;AF=0.000125098 GT:DR:DV 0/0:215803:27 +chr20 4685835 18 TTTTTAAACGGAGCGCAT N . PASS IMPRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4685853;STD_quant_start=8.629290;STD_quant_stop=10.044849;Kurtosis_quant_start=-1.667698;Kurtosis_quant_stop=-1.768586;SVTYPE=DEL;SUPTYPE=AL;SVLEN=-18;STRANDS=+-;STRANDS2=174,25,174,25;RE=199;REF_strand=198594,17238;Strandbias_pval=0.0249927;AF=0.000922013 GT:DR:DV 0/0:215633:199 +chr20 4685930 19 TGGTCAGTGTCCTTTCTACGCC N . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4685959;STD_quant_start=9.138171;STD_quant_stop=8.853401;Kurtosis_quant_start=-1.912636;Kurtosis_quant_stop=-1.865013;SVTYPE=DEL;SUPTYPE=AL,NR;SVLEN=-29;STRANDS=+-;STRANDS2=141,22,141,22;RE=163;REF_strand=198583,17265;Strandbias_pval=0.0138321;AF=0.000755161 GT:DR:DV 0/0:215685:163 +chr20 4685989 20 TAAATATTAATCTCAATC N . STRANDBIAS IMPRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4686016;STD_quant_start=10.803116;STD_quant_stop=11.316942;Kurtosis_quant_start=-2.026565;Kurtosis_quant_stop=-2.163018;SVTYPE=DEL;SUPTYPE=AL;SVLEN=-27;STRANDS=+-;STRANDS2=60,22,60,22;RE=82;REF_strand=198411,17282;Strandbias_pval=3.35709e-07;AF=0.00038017 GT:DR:DV 0/0:215611:82 +chr20 4685989 21 TTCATAAATATTAATCTCAATCCAGGTTAAGCAAAATTTTTTGCTCTCCTCTTTAGAAATTTCTGGTTGCCAAAGTT N . PASS IMPRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4686065;STD_quant_start=20.818261;STD_quant_stop=18.373895;Kurtosis_quant_start=-0.351817;Kurtosis_quant_stop=1.078616;SVTYPE=DEL;SUPTYPE=AL;SVLEN=-76;STRANDS=+-;STRANDS2=7,3,7,3;RE=10;REF_strand=198300,17295;Strandbias_pval=0.0403679;AF=4.63833e-05 GT:DR:DV 0/0:215585:10 +chr20 4686021 22 N TTTTTTTTTTTTTGTTTTTTT . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4686030;STD_quant_start=3.924283;STD_quant_stop=7.293833;Kurtosis_quant_start=-0.679233;Kurtosis_quant_stop=-0.914373;SVTYPE=INS;SUPTYPE=AL;SVLEN=12;STRANDS=+-;STRANDS2=15,0,15,0;RE=15;REF_strand=198300,17289;Strandbias_pval=0.626751;AF=6.95768e-05 GT:DR:DV 0/0:215574:15 +chr20 4686075 23 CCTCATTCCTGAG N . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4686088;STD_quant_start=3.402205;STD_quant_stop=4.782128;Kurtosis_quant_start=-1.279849;Kurtosis_quant_stop=-1.373154;SVTYPE=DEL;SUPTYPE=AL;SVLEN=-13;STRANDS=+-;STRANDS2=287,33,287,33;RE=320;REF_strand=198057,17318;Strandbias_pval=0.148536;AF=0.00148578 GT:DR:DV 0/0:215055:320 +chr20 4686129 24 GGAGCTTTGGGCCGA N . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4686142;STD_quant_start=2.512040;STD_quant_stop=2.157585;Kurtosis_quant_start=0.113758;Kurtosis_quant_stop=1.383343;SVTYPE=DEL;SUPTYPE=AL,NR;SVLEN=-13;STRANDS=+-;STRANDS2=52,6,52,6;RE=58;REF_strand=197823,17336;Strandbias_pval=0.468112;AF=0.000269568 GT:DR:DV 0/0:215101:58 +chr20 4686134 25 N TTTTTTTTTTTTTTTT . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4686134;STD_quant_start=1.439246;STD_quant_stop=5.464169;Kurtosis_quant_start=-1.581999;Kurtosis_quant_stop=-1.688649;SVTYPE=INS;SUPTYPE=AL;SVLEN=13;STRANDS=+-;STRANDS2=28,0,28,0;RE=28;REF_strand=197816,17336;Strandbias_pval=0.165458;AF=0.000130141 GT:DR:DV 0/0:215124:28 +chr20 4686162 26 N GGGATGAGGGGAT . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4686163;STD_quant_start=0.000000;STD_quant_stop=1.755942;Kurtosis_quant_start=0.099319;Kurtosis_quant_stop=-0.200217;SVTYPE=INS;SUPTYPE=AL;SVLEN=12;STRANDS=+-;STRANDS2=23,1,23,1;RE=24;REF_strand=197710,17340;Strandbias_pval=0.717698;AF=0.000111602 GT:DR:DV 0/0:215026:24 +chr20 4686262 27 CTCATTCCCGGCCCTGCTTGGCAGCGCTGCAC N . PASS IMPRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4686301;STD_quant_start=14.142414;STD_quant_stop=18.571420;Kurtosis_quant_start=-1.842589;Kurtosis_quant_stop=-1.873931;SVTYPE=DEL;SUPTYPE=AL;SVLEN=-39;STRANDS=+-;STRANDS2=229,26,229,26;RE=255;REF_strand=197046,17379;Strandbias_pval=0.2076;AF=0.00118923 GT:DR:DV 0/0:214170:255 +chr20 4686249 28 N TTTTTTTTTTT . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4686255;STD_quant_start=0.000000;STD_quant_stop=4.456135;Kurtosis_quant_start=-0.700885;Kurtosis_quant_stop=-0.721431;SVTYPE=INS;SUPTYPE=AL;SVLEN=11;STRANDS=+-;STRANDS2=27,2,27,2;RE=29;REF_strand=197229,17367;Strandbias_pval=1;AF=0.000135138 GT:DR:DV 0/0:214567:29 +chr20 4686292 29 GCACAGAGTGT N . STRANDBIAS IMPRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4686341;STD_quant_start=11.521960;STD_quant_stop=7.336363;Kurtosis_quant_start=-1.977570;Kurtosis_quant_stop=-1.737848;SVTYPE=DEL;SUPTYPE=AL,NR;SVLEN=-49;STRANDS=+-;STRANDS2=137,44,137,44;RE=181;REF_strand=196858,17387;Strandbias_pval=3.60206e-11;AF=0.000844827 GT:DR:DV 0/0:214064:181 +chr20 4686356 30 N CCCGCACGCTGGCCT . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4686363;STD_quant_start=9.954898;STD_quant_stop=9.170605;Kurtosis_quant_start=-0.822541;Kurtosis_quant_stop=-0.627363;SVTYPE=INS;SUPTYPE=AL;SVLEN=11;STRANDS=+-;STRANDS2=12,2,12,2;RE=14;REF_strand=196623,17405;Strandbias_pval=0.317055;AF=6.5412e-05 GT:DR:DV 0/0:214014:14 +chr20 4686419 31 N CCCCCCCCCCCCCCC . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4686422;STD_quant_start=8.111720;STD_quant_stop=8.160882;Kurtosis_quant_start=-1.678369;Kurtosis_quant_stop=-1.644171;SVTYPE=INS;SUPTYPE=AL;SVLEN=15;STRANDS=+-;STRANDS2=15,3,15,3;RE=18;REF_strand=196230,17424;Strandbias_pval=0.17724;AF=8.42484e-05 GT:DR:DV 0/0:213636:18 +chr20 4686426 32 CCTCGGCCCCG N . STRANDBIAS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4686437;STD_quant_start=4.661627;STD_quant_stop=4.544650;Kurtosis_quant_start=-1.377361;Kurtosis_quant_stop=-1.540285;SVTYPE=DEL;SUPTYPE=AL;SVLEN=-11;STRANDS=+-;STRANDS2=114,43,114,43;RE=157;REF_strand=196173,17425;Strandbias_pval=9.82933e-13;AF=0.000735026 GT:DR:DV 0/0:213441:157 +chr20 4686486 33 CTTCTCCTCTCCTCACGA N . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4686497;STD_quant_start=2.506368;STD_quant_stop=2.956054;Kurtosis_quant_start=-0.539083;Kurtosis_quant_stop=1.458892;SVTYPE=DEL;SUPTYPE=AL,NR;SVLEN=-11;STRANDS=+-;STRANDS2=265,34,265,34;RE=299;REF_strand=195814,17444;Strandbias_pval=0.0562093;AF=0.00140206 GT:DR:DV 0/0:212959:299 +chr20 4686606 34 CGGCCGGGCGG N . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4686620;STD_quant_start=4.189935;STD_quant_stop=3.704352;Kurtosis_quant_start=-0.190418;Kurtosis_quant_stop=-0.184702;SVTYPE=DEL;SUPTYPE=AL;SVLEN=-14;STRANDS=+-;STRANDS2=61,11,61,11;RE=72;REF_strand=195198,17480;Strandbias_pval=0.0481751;AF=0.00033854 GT:DR:DV 0/0:212606:72 +chr20 4686670 35 CGCGTCTCGGG N . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4686681;STD_quant_start=1.914854;STD_quant_stop=2.188122;Kurtosis_quant_start=-0.414934;Kurtosis_quant_stop=-0.207072;SVTYPE=DEL;SUPTYPE=AL;SVLEN=-11;STRANDS=+-;STRANDS2=55,12,55,12;RE=67;REF_strand=194945,17513;Strandbias_pval=0.0113094;AF=0.000315356 GT:DR:DV 0/0:212391:67 +chr20 4686765 36 GGGGGGCTGGGGGAGCTGGCGGAGCC N . STRANDBIAS IMPRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4686821;STD_quant_start=4.722288;STD_quant_stop=13.957077;Kurtosis_quant_start=-1.555816;Kurtosis_quant_stop=-1.908362;SVTYPE=DEL;SUPTYPE=AL,NR;SVLEN=-56;STRANDS=+-;STRANDS2=11,7,11,7;RE=18;REF_strand=194333,17569;Strandbias_pval=0.000376835;AF=8.49449e-05 GT:DR:DV 0/0:211884:18 +chr20 4686891 37 GGGCCGCCAGCGGGCTCCGCAGGGCGCGGGGCGGGGAGGGGCGCCTGGGGGCCGCGGGGCTCGCGCTCCCCGCCCGTTGGCCGCCCCTCGGAGGCCGAGATCG N . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4686956;STD_quant_start=8.485281;STD_quant_stop=4.711688;Kurtosis_quant_start=-1.114855;Kurtosis_quant_stop=0.770261;SVTYPE=DEL;SUPTYPE=AL;SVLEN=-65;STRANDS=+-;STRANDS2=10,3,10,3;RE=13;REF_strand=193714,17606;Strandbias_pval=0.0879808;AF=6.15181e-05 GT:DR:DV 0/0:211307:13 +chr20 4686918 38 N GGGGGGAGGGGGGA . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4686918;STD_quant_start=2.863564;STD_quant_stop=3.987480;Kurtosis_quant_start=-1.571348;Kurtosis_quant_stop=-1.722562;SVTYPE=INS;SUPTYPE=AL;SVLEN=11;STRANDS=+-;STRANDS2=19,2,19,2;RE=21;REF_strand=193744,17608;Strandbias_pval=0.692842;AF=9.93603e-05 GT:DR:DV 0/0:211331:21 +chr20 4686960 39 CCGCCCGTTGG N . STRANDBIAS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4686971;STD_quant_start=6.335549;STD_quant_stop=5.570078;Kurtosis_quant_start=-1.597036;Kurtosis_quant_stop=-1.720519;SVTYPE=DEL;SUPTYPE=AL;SVLEN=-11;STRANDS=+-;STRANDS2=331,58,331,58;RE=389;REF_strand=193494,17619;Strandbias_pval=1.97475e-05;AF=0.00184262 GT:DR:DV 0/0:210724:389 +chr20 4686972 40 N CCAGCCCCTGTTG . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4686974;STD_quant_start=3.941886;STD_quant_stop=4.811844;Kurtosis_quant_start=-1.826431;Kurtosis_quant_stop=-1.635604;SVTYPE=INS;SUPTYPE=AL;SVLEN=11;STRANDS=+-;STRANDS2=26,1,26,1;RE=27;REF_strand=193462,17623;Strandbias_pval=0.723279;AF=0.000127911 GT:DR:DV 0/0:211058:27 +chr20 4686997 41 CCCAGAACGCC N . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4687008;STD_quant_start=5.342072;STD_quant_stop=6.220781;Kurtosis_quant_start=-1.477900;Kurtosis_quant_stop=-0.980598;SVTYPE=DEL;SUPTYPE=AL,NR;SVLEN=-11;STRANDS=+-;STRANDS2=189,23,189,23;RE=212;REF_strand=193314,17636;Strandbias_pval=0.212404;AF=0.00100498 GT:DR:DV 0/0:210738:212 +chr20 4687051 42 N GGGGGGGGGGG . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4687051;STD_quant_start=1.945691;STD_quant_stop=4.598136;Kurtosis_quant_start=-1.535668;Kurtosis_quant_stop=-1.371399;SVTYPE=INS;SUPTYPE=AL;SVLEN=11;STRANDS=+-;STRANDS2=26,3,26,3;RE=29;REF_strand=193096,17662;Strandbias_pval=0.731612;AF=0.000137599 GT:DR:DV 0/0:210729:29 +chr20 4687041 43 GAGAGGGGCGCCCGCCGGGGGAGTT N . STRANDBIAS IMPRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4687087;STD_quant_start=11.917472;STD_quant_stop=8.148138;Kurtosis_quant_start=-1.940085;Kurtosis_quant_stop=-1.625654;SVTYPE=DEL;SUPTYPE=AL,NR;SVLEN=-46;STRANDS=+-;STRANDS2=227,79,227,79;RE=306;REF_strand=193002,17665;Strandbias_pval=1.28673e-19;AF=0.00145253 GT:DR:DV 0/0:210361:306 +chr20 4687095 44 CTCGGTGCCTCCCGCCGCAGCT N . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4687123;STD_quant_start=3.341656;STD_quant_stop=4.000000;Kurtosis_quant_start=-1.308668;Kurtosis_quant_stop=-1.466072;SVTYPE=DEL;SUPTYPE=AL;SVLEN=-28;STRANDS=+-;STRANDS2=24,1,24,1;RE=25;REF_strand=192767,17680;Strandbias_pval=0.718618;AF=0.000118795 GT:DR:DV 0/0:210422:25 +chr20 4687199 45 ACCGCCTGGAGAA N . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4687217;STD_quant_start=3.566822;STD_quant_stop=1.563472;Kurtosis_quant_start=-0.977603;Kurtosis_quant_stop=0.821992;SVTYPE=DEL;SUPTYPE=AL;SVLEN=-18;STRANDS=+-;STRANDS2=70,3,70,3;RE=73;REF_strand=192315,17692;Strandbias_pval=0.286586;AF=0.000347607 GT:DR:DV 0/0:209934:73 +chr20 4687215 46 GAAGCGGCCCACGCGGACTGACGGGCGGGGGCGGGGCCTCGGGCCTCGGCGGGGGCGGGGTCCGGGGAGGCCCCACCCTCTGTTCTCCAGGGGCGGGGAGAGAGGAGCTGCAGG N . PASS IMPRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4687325;STD_quant_start=14.166863;STD_quant_stop=17.807302;Kurtosis_quant_start=-0.855457;Kurtosis_quant_stop=-0.901175;SVTYPE=DEL;SUPTYPE=AL;SVLEN=-110;STRANDS=+-;STRANDS2=11,2,11,2;RE=13;REF_strand=192013,17691;Strandbias_pval=0.301164;AF=6.19921e-05 GT:DR:DV 0/0:209691:13 +chr20 4687235 47 GGGCGGGGGCG N . STRANDBIAS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4687247;STD_quant_start=4.480728;STD_quant_stop=3.624171;Kurtosis_quant_start=-0.936939;Kurtosis_quant_stop=-1.752433;SVTYPE=DEL;SUPTYPE=AL;SVLEN=-12;STRANDS=+-;STRANDS2=86,18,86,18;RE=104;REF_strand=192166,17692;Strandbias_pval=0.00374966;AF=0.000495573 GT:DR:DV 0/0:209754:104 +chr20 4687275 48 CCGGGGAGGCC N . STRANDBIAS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4687286;STD_quant_start=5.832166;STD_quant_stop=6.143469;Kurtosis_quant_start=-1.455321;Kurtosis_quant_stop=-1.418474;SVTYPE=DEL;SUPTYPE=AL,NR;SVLEN=-11;STRANDS=+-;STRANDS2=620,86,620,86;RE=706;REF_strand=191914,17691;Strandbias_pval=0.00067667;AF=0.00336824 GT:DR:DV 0/0:208899:706 +chr20 4687322 49 AGCTGCAGGTCTGCGGCCTGGCCCCAGGTGCGATGGCGGAC N . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4687361;STD_quant_start=4.516636;STD_quant_stop=8.843076;Kurtosis_quant_start=1.699914;Kurtosis_quant_stop=-1.310726;SVTYPE=DEL;SUPTYPE=AL;SVLEN=-39;STRANDS=+-;STRANDS2=12,1,12,1;RE=13;REF_strand=191635,17689;Strandbias_pval=1;AF=6.21047e-05 GT:DR:DV 0/0:209311:13 +chr20 4687385 50 N CAGCCCGGCGA . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4687387;STD_quant_start=4.983305;STD_quant_stop=4.092676;Kurtosis_quant_start=-1.884924;Kurtosis_quant_stop=-1.837871;SVTYPE=INS;SUPTYPE=AL;SVLEN=11;STRANDS=+-;STRANDS2=22,2,22,2;RE=24;REF_strand=191424,17688;Strandbias_pval=1;AF=0.000114771 GT:DR:DV 0/0:209088:24 +chr20 4687442 51 CCTTGGGTCACCGGTCTCCCCACCTGTGCGGCAGGCGCCTTCACGTTTCATTATTAAACAATGGG N . PASS IMPRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4687517;STD_quant_start=10.526158;STD_quant_stop=5.291503;Kurtosis_quant_start=-1.121629;Kurtosis_quant_stop=-1.338714;SVTYPE=DEL;SUPTYPE=AL;SVLEN=-75;STRANDS=+-;STRANDS2=17,1,17,1;RE=18;REF_strand=190988,17685;Strandbias_pval=1;AF=8.62594e-05 GT:DR:DV 0/0:208655:18 +chr20 4687566 52 TTTGAGGTGGCTGTAGGAAATAGATTT N . STRANDBIAS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4687594;STD_quant_start=6.217087;STD_quant_stop=3.614584;Kurtosis_quant_start=-1.978927;Kurtosis_quant_stop=0.848130;SVTYPE=DEL;SUPTYPE=AL,NR;SVLEN=-28;STRANDS=+-;STRANDS2=67,25,67,25;RE=92;REF_strand=190327,17684;Strandbias_pval=1.30405e-07;AF=0.000442284 GT:DR:DV 0/0:207919:92 +chr20 4687590 53 N TTTTTTTTTTT . STRANDBIAS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4687590;STD_quant_start=0.000000;STD_quant_stop=1.469694;Kurtosis_quant_start=5.569528;Kurtosis_quant_stop=0.922248;SVTYPE=INS;SUPTYPE=AL;SVLEN=11;STRANDS=+-;STRANDS2=100,1,100,1;RE=101;REF_strand=190224,17684;Strandbias_pval=0.00212072;AF=0.000485792 GT:DR:DV 0/0:207807:101 +chr20 4687605 54 TCGCCATCGCAGAGCCACAGCT N . STRANDBIAS IMPRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4687655;STD_quant_start=17.714544;STD_quant_stop=9.721983;Kurtosis_quant_start=-1.894930;Kurtosis_quant_stop=-1.919249;SVTYPE=DEL;SUPTYPE=AL;SVLEN=-50;STRANDS=+-;STRANDS2=195,41,195,41;RE=236;REF_strand=190051,17683;Strandbias_pval=1.15868e-05;AF=0.00113607 GT:DR:DV 0/0:207498:236 +chr20 4687726 55 TCTTCATGGCCG N . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4687738;STD_quant_start=2.928984;STD_quant_stop=2.942430;Kurtosis_quant_start=-0.902921;Kurtosis_quant_stop=-0.980399;SVTYPE=DEL;SUPTYPE=AL;SVLEN=-12;STRANDS=+-;STRANDS2=139,13,139,13;RE=152;REF_strand=189466,17680;Strandbias_pval=1;AF=0.000733782 GT:DR:DV 0/0:206994:152 +chr20 4687830 56 N . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4687841;STD_quant_start=3.916686;STD_quant_stop=4.855355;Kurtosis_quant_start=-1.329767;Kurtosis_quant_stop=-0.264696;SVTYPE=DEL;SUPTYPE=AL;SVLEN=-11;STRANDS=+-;STRANDS2=88,6,88,6;RE=94;REF_strand=188891,17676;Strandbias_pval=0.580169;AF=0.000455058 GT:DR:DV 0/0:206473:94 +chr20 4687869 57 N . STRANDBIAS IMPRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4687909;STD_quant_start=9.453234;STD_quant_stop=12.427974;Kurtosis_quant_start=-1.826891;Kurtosis_quant_stop=-2.002236;SVTYPE=DEL;SUPTYPE=AL,NR;SVLEN=-40;STRANDS=+-;STRANDS2=90,20,90,20;RE=110;REF_strand=188602,17673;Strandbias_pval=0.00162405;AF=0.000533269 GT:DR:DV 0/0:206165:110 +chr20 4687914 58 TCAACAACGCT N . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4687925;STD_quant_start=1.341641;STD_quant_stop=1.807392;Kurtosis_quant_start=2.650476;Kurtosis_quant_stop=2.870736;SVTYPE=DEL;SUPTYPE=AL;SVLEN=-11;STRANDS=+-;STRANDS2=23,7,23,7;RE=30;REF_strand=188393,17670;Strandbias_pval=0.0118931;AF=0.000145587 GT:DR:DV 0/0:206033:30 +chr20 4687913 59 N AAAAAAAAAAAAAAAAAAAAA . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4687922;STD_quant_start=7.483315;STD_quant_stop=7.042727;Kurtosis_quant_start=-1.719857;Kurtosis_quant_stop=-1.344155;SVTYPE=INS;SUPTYPE=AL;SVLEN=11;STRANDS=+-;STRANDS2=13,4,13,4;RE=17;REF_strand=188410,17670;Strandbias_pval=0.0520474;AF=8.24922e-05 GT:DR:DV 0/0:206063:17 +chr20 4688013 60 N . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4688025;STD_quant_start=5.196152;STD_quant_stop=4.505552;Kurtosis_quant_start=-1.594248;Kurtosis_quant_stop=-1.716931;SVTYPE=DEL;SUPTYPE=AL;SVLEN=-12;STRANDS=+-;STRANDS2=10,1,10,1;RE=11;REF_strand=186802,17390;Strandbias_pval=1;AF=5.38709e-05 GT:DR:DV 0/0:204181:11 diff --git a/SVs_sniffles/vcf/55048_bodySnif.vcf b/SVs_sniffles/vcf/55048_bodySnif.vcf new file mode 100644 index 0000000..c0ac116 --- /dev/null +++ b/SVs_sniffles/vcf/55048_bodySnif.vcf @@ -0,0 +1,36 @@ +##fileformat=VCFv4.1 +##source=Sniffles +##fileDate=20210810:56:21 AMef_minus +##contig= +##ALT= +##ALT= +##ALT= +##ALT= +##ALT= +##ALT= +##FILTER= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##FORMAT= +##FORMAT= +##FORMAT= +#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT bamfilt/55048_f.bam diff --git a/SVs_sniffles/vcf/55048_promoterSnif.vcf b/SVs_sniffles/vcf/55048_promoterSnif.vcf new file mode 100644 index 0000000..a2a5ccb --- /dev/null +++ b/SVs_sniffles/vcf/55048_promoterSnif.vcf @@ -0,0 +1,97 @@ +##fileformat=VCFv4.1 +##source=Sniffles +##fileDate=20210811:40:33 AMef_minus +##contig= +##ALT= +##ALT= +##ALT= +##ALT= +##ALT= +##ALT= +##FILTER= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##FORMAT= +##FORMAT= +##FORMAT= +#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT promoterbamfilt/55048_f.bam +chr20 4685130 0 TTGTACCCCTCCC N . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4685149;STD_quant_start=7.345949;STD_quant_stop=6.928203;Kurtosis_quant_start=-1.730337;Kurtosis_quant_stop=-1.577246;SVTYPE=DEL;SUPTYPE=AL;SVLEN=-19;STRANDS=+-;STRANDS2=71,37,71,37;RE=108;REF_strand=121597,106025;Strandbias_pval=0.0118158;AF=0.000474471 GT:DR:DV 0/0:227514:108 +chr20 4685224 1 TTTTTTTTTTT N . STRANDBIAS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4685235;STD_quant_start=0.229039;STD_quant_stop=1.573344;Kurtosis_quant_start=0.629058;Kurtosis_quant_stop=1.684474;SVTYPE=DEL;SUPTYPE=AL,NR;SVLEN=-11;STRANDS=+-;STRANDS2=578,643,578,643;RE=1221;REF_strand=121654,106365;Strandbias_pval=2.98633e-05;AF=0.00535482 GT:DR:DV 0/0:226798:1221 +chr20 4685224 2 N TTTTTTTTTTTTT . STRANDBIAS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4685224;STD_quant_start=0.000000;STD_quant_stop=1.130534;Kurtosis_quant_start=77.071941;Kurtosis_quant_stop=2.746675;SVTYPE=INS;SUPTYPE=AL;SVLEN=11;STRANDS=+-;STRANDS2=3592,127,3592,127;RE=3719;REF_strand=121654,106336;Strandbias_pval=0;AF=0.0163121 GT:DR:DV 0/0:224271:3719 +chr20 4685333 3 CTCCTGGGCTCAAGCAATCCTCCCAT N . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4685365;STD_quant_start=4.647580;STD_quant_stop=7.141428;Kurtosis_quant_start=0.474442;Kurtosis_quant_stop=0.290393;SVTYPE=DEL;SUPTYPE=AL;SVLEN=-32;STRANDS=+-;STRANDS2=8,5,8,5;RE=13;REF_strand=121741,106907;Strandbias_pval=0.591517;AF=5.6856e-05 GT:DR:DV 0/0:228635:13 +chr20 4685367 4 N TTTTTCTCTGCCTGTTT . STRANDBIAS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4685373;STD_quant_start=3.098387;STD_quant_stop=5.128353;Kurtosis_quant_start=-0.774622;Kurtosis_quant_stop=-0.928502;SVTYPE=INS;SUPTYPE=AL;SVLEN=11;STRANDS=+-;STRANDS2=17,2,17,2;RE=19;REF_strand=121742,106989;Strandbias_pval=0.00183427;AF=8.3067e-05 GT:DR:DV 0/0:228712:19 +chr20 4685413 5 N TTTTTTTATTTT . STRANDBIAS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4685416;STD_quant_start=0.000000;STD_quant_stop=2.714749;Kurtosis_quant_start=-0.989647;Kurtosis_quant_stop=0.863895;SVTYPE=INS;SUPTYPE=AL;SVLEN=11;STRANDS=+-;STRANDS2=134,13,134,13;RE=147;REF_strand=121744,107116;Strandbias_pval=2.63833e-23;AF=0.000642314 GT:DR:DV 0/0:228713:147 +chr20 4685425 6 AACTCCTGAGCTCAAGC N . PASS IMPRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4685487;STD_quant_start=29.448260;STD_quant_stop=16.201852;Kurtosis_quant_start=-0.891168;Kurtosis_quant_stop=-0.821984;SVTYPE=DEL;SUPTYPE=AL;SVLEN=-62;STRANDS=+-;STRANDS2=9,1,9,1;RE=10;REF_strand=121745,107237;Strandbias_pval=0.0239737;AF=4.36716e-05 GT:DR:DV 0/0:228972:10 +chr20 4685441 7 TGGGGTCTCACTATGTTG N . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4685453;STD_quant_start=1.595448;STD_quant_stop=0.852803;Kurtosis_quant_start=1.047502;Kurtosis_quant_stop=-0.879249;SVTYPE=DEL;SUPTYPE=AL;SVLEN=-12;STRANDS=+-;STRANDS2=14,9,14,9;RE=23;REF_strand=121746,107233;Strandbias_pval=0.53406;AF=0.000100446 GT:DR:DV 0/0:228956:23 +chr20 4685467 8 N AAAAAAAAAAA . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4685470;STD_quant_start=5.504544;STD_quant_stop=5.422177;Kurtosis_quant_start=-1.887687;Kurtosis_quant_stop=-1.501161;SVTYPE=INS;SUPTYPE=AL;SVLEN=12;STRANDS=+-;STRANDS2=8,12,8,12;RE=20;REF_strand=121746,107294;Strandbias_pval=0.26798;AF=8.7321e-05 GT:DR:DV 0/0:229020:20 +chr20 4685526 9 CTGGCTGTCAACATTCTTAAATCTCTTTCCTTACATGCTT N . STRANDBIAS IMPRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4685579;STD_quant_start=14.233402;STD_quant_stop=7.778175;Kurtosis_quant_start=-2.012172;Kurtosis_quant_stop=-1.798723;SVTYPE=DEL;SUPTYPE=AL;SVLEN=-53;STRANDS=+-;STRANDS2=108,48,108,48;RE=156;REF_strand=121749,107499;Strandbias_pval=5.26963e-05;AF=0.000680486 GT:DR:DV 0/0:229092:156 +chr20 4685598 10 CTAGGAGACTAGATGT N . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4685617;STD_quant_start=3.605551;STD_quant_stop=3.269174;Kurtosis_quant_start=-0.673433;Kurtosis_quant_stop=-0.822226;SVTYPE=DEL;SUPTYPE=AL;SVLEN=-19;STRANDS=+-;STRANDS2=17,15,17,15;RE=32;REF_strand=121753,107625;Strandbias_pval=1;AF=0.000139508 GT:DR:DV 0/0:229346:32 +chr20 4685701 11 N CCCCCCCCCCCCCCCCCCC . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4685714;STD_quant_start=6.220932;STD_quant_stop=7.021396;Kurtosis_quant_start=-1.689311;Kurtosis_quant_stop=-1.777447;SVTYPE=INS;SUPTYPE=AL;SVLEN=11;STRANDS=+-;STRANDS2=8,13,8,13;RE=21;REF_strand=121756,107894;Strandbias_pval=0.193661;AF=9.14435e-05 GT:DR:DV 0/0:229629:21 +chr20 4685777 12 CGCAAGAACACACCAC N . STRANDBIAS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4685794;STD_quant_start=4.140393;STD_quant_stop=4.750940;Kurtosis_quant_start=-0.970300;Kurtosis_quant_stop=-1.063680;SVTYPE=DEL;SUPTYPE=AL;SVLEN=-17;STRANDS=+-;STRANDS2=81,32,81,32;RE=113;REF_strand=121758,108085;Strandbias_pval=6.3352e-05;AF=0.00049164 GT:DR:DV 0/0:229730:113 +chr20 4685819 13 AATGTGCAAACACGGG N . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4685842;STD_quant_start=3.415650;STD_quant_stop=3.734226;Kurtosis_quant_start=-0.179779;Kurtosis_quant_stop=-1.517864;SVTYPE=DEL;SUPTYPE=AL;SVLEN=-23;STRANDS=+-;STRANDS2=34,39,34,39;RE=73;REF_strand=121760,108206;Strandbias_pval=0.292648;AF=0.000317438 GT:DR:DV 0/0:229893:73 +chr20 4685835 14 N TTTTTTTTTTTTT . STRANDBIAS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4685852;STD_quant_start=7.916228;STD_quant_stop=5.715476;Kurtosis_quant_start=-1.720927;Kurtosis_quant_stop=-1.128506;SVTYPE=INS;SUPTYPE=AL;SVLEN=12;STRANDS=+-;STRANDS2=29,2,29,2;RE=31;REF_strand=121760,108243;Strandbias_pval=1.58257e-06;AF=0.000134781 GT:DR:DV 0/0:229972:31 +chr20 4686017 15 AAAATTTTTTG N . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4686028;STD_quant_start=2.275647;STD_quant_stop=3.262339;Kurtosis_quant_start=2.056156;Kurtosis_quant_stop=-0.140888;SVTYPE=DEL;SUPTYPE=AL,NR;SVLEN=-11;STRANDS=+-;STRANDS2=33,24,33,24;RE=57;REF_strand=121464,108700;Strandbias_pval=0.507613;AF=0.00024765 GT:DR:DV 0/0:230107:57 +chr20 4686021 16 N TTTTTTTTTTTT . STRANDBIAS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4686022;STD_quant_start=3.741657;STD_quant_stop=6.468860;Kurtosis_quant_start=-1.859276;Kurtosis_quant_stop=-1.238362;SVTYPE=INS;SUPTYPE=AL;SVLEN=11;STRANDS=+-;STRANDS2=23,4,23,4;RE=27;REF_strand=121456,108696;Strandbias_pval=0.000712201;AF=0.000117314 GT:DR:DV 0/0:230125:27 +chr20 4686075 17 CTCATTCCTGAG N . STRANDBIAS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4686088;STD_quant_start=3.977098;STD_quant_stop=5.238541;Kurtosis_quant_start=-1.404492;Kurtosis_quant_stop=-1.567715;SVTYPE=DEL;SUPTYPE=AL;SVLEN=-13;STRANDS=+-;STRANDS2=148,61,148,61;RE=209;REF_strand=121219,108842;Strandbias_pval=1.05767e-07;AF=0.000908455 GT:DR:DV 0/0:229852:209 +chr20 4686095 18 N AACGCTGCTTA . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4686101;STD_quant_start=4.883252;STD_quant_stop=3.833055;Kurtosis_quant_start=-1.021555;Kurtosis_quant_stop=-0.945712;SVTYPE=INS;SUPTYPE=AL;SVLEN=11;STRANDS=+-;STRANDS2=17,9,17,9;RE=26;REF_strand=121161,108888;Strandbias_pval=0.239658;AF=0.000113019 GT:DR:DV 0/0:230023:26 +chr20 4686088 19 CCTTTCATTTTCTCGATTTCTCCATTATGTAACGGGGAGCTGGAGCTTTGGGCCGAATTTCCAATTAAAGATGATTTTTACAGTCAATGAGCCA N . PASS IMPRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4686173;STD_quant_start=15.883954;STD_quant_stop=23.513826;Kurtosis_quant_start=0.037372;Kurtosis_quant_stop=-0.895365;SVTYPE=DEL;SUPTYPE=AL,NR;SVLEN=-85;STRANDS=+-;STRANDS2=4,7,4,7;RE=11;REF_strand=121000,108965;Strandbias_pval=0.369235;AF=4.78334e-05 GT:DR:DV 0/0:229954:11 +chr20 4686134 20 N TTTTTTTTTTTTT . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4686134;STD_quant_start=0.957427;STD_quant_stop=4.163332;Kurtosis_quant_start=-1.284438;Kurtosis_quant_stop=-1.661837;SVTYPE=INS;SUPTYPE=AL;SVLEN=12;STRANDS=+-;STRANDS2=16,8,16,8;RE=24;REF_strand=120986,108952;Strandbias_pval=0.220033;AF=0.000104376 GT:DR:DV 0/0:229914:24 +chr20 4686195 21 TGGCACCCGCAGGCGG N . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4686211;STD_quant_start=4.096069;STD_quant_stop=4.006938;Kurtosis_quant_start=-0.515870;Kurtosis_quant_stop=-0.386550;SVTYPE=DEL;SUPTYPE=AL,NR;SVLEN=-16;STRANDS=+-;STRANDS2=67,42,67,42;RE=109;REF_strand=120660,109148;Strandbias_pval=0.0681444;AF=0.000474309 GT:DR:DV 0/0:229699:109 +chr20 4686162 22 N TTTTTTTTTTTTTTTTTTTTTTTTTTTTT . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4686172;STD_quant_start=3.016621;STD_quant_stop=6.284903;Kurtosis_quant_start=0.077837;Kurtosis_quant_stop=-0.141119;SVTYPE=INS;SUPTYPE=AL;SVLEN=13;STRANDS=+-;STRANDS2=13,3,13,3;RE=16;REF_strand=120832,109048;Strandbias_pval=0.0239193;AF=6.96015e-05 GT:DR:DV 0/0:229864:16 +chr20 4686230 23 TCAAGCGAATC N . STRANDBIAS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4686241;STD_quant_start=2.813234;STD_quant_stop=3.202677;Kurtosis_quant_start=2.385058;Kurtosis_quant_stop=0.489108;SVTYPE=DEL;SUPTYPE=AL;SVLEN=-11;STRANDS=+-;STRANDS2=23,48,23,48;RE=71;REF_strand=120482,109233;Strandbias_pval=0.000785141;AF=0.000309079 GT:DR:DV 0/0:229644:71 +chr20 4686249 24 N TTTTTTTTTTTTTTTTTTTTTTTTTTTT . STRANDBIAS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4686264;STD_quant_start=7.157883;STD_quant_stop=9.245030;Kurtosis_quant_start=-1.789612;Kurtosis_quant_stop=-1.733222;SVTYPE=INS;SUPTYPE=AL;SVLEN=13;STRANDS=+-;STRANDS2=28,6,28,6;RE=34;REF_strand=120318,109287;Strandbias_pval=0.000423443;AF=0.00014808 GT:DR:DV 0/0:229571:34 +chr20 4686278 25 CATTCCCGGCCCTGCTTGGCAGCGCTGCACCCTTTAACTTAAACCTCGGCCGGCCGCCCGCCGGGGGCACAGAGTGTGCGCCGGGCCGCGCGGCAATTGGTC N . STRANDBIAS IMPRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4686366;STD_quant_start=13.729530;STD_quant_stop=9.027735;Kurtosis_quant_start=0.077137;Kurtosis_quant_stop=-0.752391;SVTYPE=DEL;SUPTYPE=AL,NR;SVLEN=-88;STRANDS=+-;STRANDS2=0,11,0,11;RE=11;REF_strand=119908,109449;Strandbias_pval=0.000292304;AF=4.79602e-05 GT:DR:DV 0/0:229346:11 +chr20 4686310 26 CGGCCGGCCGC N . STRANDBIAS IMPRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4686351;STD_quant_start=12.065146;STD_quant_stop=16.270892;Kurtosis_quant_start=-1.750183;Kurtosis_quant_stop=-1.821574;SVTYPE=DEL;SUPTYPE=AL;SVLEN=-41;STRANDS=+-;STRANDS2=126,185,126,185;RE=311;REF_strand=119841,109469;Strandbias_pval=4.01158e-05;AF=0.00135624 GT:DR:DV 0/0:228999:311 +chr20 4686326 27 GGGGGCACAGAGTGTGCGCCGGGCCGCGCGGCAATTGGTCCCCGCGCCGACCTCCGCCCGCGAGCGCCGCCGCTTCCCTTCCCCGCCCCGCGTCCCTCCCCCTCGGCCCCGCGCGTCGCCTGTCCTCCGAGCCAGTCGCTGACAGCCGCGGCGCCGCGAGCTTCTCCTCTCCTCACGACCGAGGCAGGTAAACGCCCGGGGTGGGAGGAACGCGGGCGGGGGCAGGGGAGCCGCGGGGGCCGAGTGAGGACCCCGGGCCTCGGGTCCCAGGCGCAAGGGTGCCCGGCCGGGCGGGGTCGGGACCCCAGTGAGGAGGGGCCGGGGGCTGCCCCGCGGGCGCGTGACGCGTCTCGGGCCTGCCCGGCTGCGCTGGTCTCCGCTCGGGTGAGGCGGCTTGGCTTCGCTTTTCAGGTTAGGAAAGCTCCCTTTACTGCGCGTTGGGGGGCTGGGGGAGCTGGCGGAGCCCCGTTAGGGAGGTCGGTGGCGCCGGGGTGTCTCAGCGCCCCCTGCACCCCGCGCGGGTCCGGCCCAGCGGGCGATCGCTGGCGCCCAGGGAACTCCGGGAGGGCCGCCAGCGGGCTCCGCAGGGCGCGGGGCGGGGAGGGGCGCCTGGGGGCCGCGGGGCTCGCGCTCCCCGCCCGTTGGCCGCCCCTCGGAGGCCGAGATCGGGGCCCAGAACGCCCCTTGGCAAGGCCTGGCGCTTCCGCGATGCCCAGAGGGTGCTTGGGGGGATGGAGAGAGGGGCGCCCGCCG N . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4687079;STD_quant_start=0.277350;STD_quant_stop=0.620174;Kurtosis_quant_start=-1.725499;Kurtosis_quant_stop=-1.849878;SVTYPE=DEL;SUPTYPE=AL;SVLEN=-753;STRANDS=+-;STRANDS2=15,11,15,11;RE=26;REF_strand=118370,110671;Strandbias_pval=0.562999;AF=0.000113517 GT:DR:DV 0/0:229015:26 +chr20 4686392 28 CCGCCGCTTCC N . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4686405;STD_quant_start=5.934592;STD_quant_stop=5.999575;Kurtosis_quant_start=-1.236268;Kurtosis_quant_stop=-1.349118;SVTYPE=DEL;SUPTYPE=AL;SVLEN=-13;STRANDS=+-;STRANDS2=186,207,186,207;RE=393;REF_strand=119483,109648;Strandbias_pval=0.0613996;AF=0.00171518 GT:DR:DV 0/0:228738:393 +chr20 4686406 29 CCTCGGCCCCG N . STRANDBIAS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4686437;STD_quant_start=4.659364;STD_quant_stop=6.729809;Kurtosis_quant_start=-1.586383;Kurtosis_quant_stop=-1.929312;SVTYPE=DEL;SUPTYPE=AL,NR;SVLEN=-31;STRANDS=+-;STRANDS2=103,21,103,21;RE=124;REF_strand=119364,109712;Strandbias_pval=7.54515e-13;AF=0.000541305 GT:DR:DV 0/0:228952:124 +chr20 4686411 30 CCTCGGCCCCG N . STRANDBIAS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4686437;STD_quant_start=3.467238;STD_quant_stop=5.979130;Kurtosis_quant_start=-0.840818;Kurtosis_quant_stop=-0.183850;SVTYPE=DEL;SUPTYPE=AL;SVLEN=-26;STRANDS=+-;STRANDS2=23,162,23,162;RE=185;REF_strand=119357,109720;Strandbias_pval=1.22493e-29;AF=0.000807589 GT:DR:DV 0/0:228892:185 +chr20 4686441 31 N GCGGCCACGCGGCGGCGC . PASS IMPRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4686454;STD_quant_start=11.685267;STD_quant_stop=7.192167;Kurtosis_quant_start=-1.625121;Kurtosis_quant_stop=-1.895180;SVTYPE=INS;SUPTYPE=AL;SVLEN=11;STRANDS=+-;STRANDS2=12,11,12,11;RE=23;REF_strand=119237,109796;Strandbias_pval=1;AF=0.000100422 GT:DR:DV 0/0:229010:23 +chr20 4686486 32 CTTCTCCTCTCCT N . STRANDBIAS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4686497;STD_quant_start=3.341514;STD_quant_stop=4.084116;Kurtosis_quant_start=-1.092774;Kurtosis_quant_stop=-0.985751;SVTYPE=DEL;SUPTYPE=AL;SVLEN=-11;STRANDS=+-;STRANDS2=208,142,208,142;RE=350;REF_strand=119027,109917;Strandbias_pval=0.00535601;AF=0.00152876 GT:DR:DV 0/0:228594:350 +chr20 4686538 33 CGGGCGGGGGCAGGGGAGCCGCGGGGGCCGAGTGAGGACCCCGGGCCTCGGGTCCCAGGCGCAAGGGTGCCCGGCCGGGCGGGGTCGGGACCCCAGTGAGGAGGGGCCGGGGGCTGCCCCGCGGGCGCGTGACGCGTCTCGGGCCTGCCCGGCTGCGCTGGTCTCCGCTCGGGTGAGGCGGCTTGGCTTCGCTTTTCAGGTTAGGAAAGCTCCCTTTACTGCGCGTTGGGGGGCTGGGGGAGCTGGCGGAGCCCCGTTAGGGAGGTCGGTGGCGCCGGGGTGTCTCAGCGCCCCCTGCACCCCGCGCGGGTCCGGCCCAGCGGGCGATCGCTGGCGCCCAGGGAACTCCGGGAGGGCCGCCAGCGGGCTCCGCAGGGCGCGGGGCGGGGAGGGGCGCCTGGGGGCCGCGGGGCTCGCGCTCCCCGCCCGTTGGCCGCCCCTCGGAGGCCGAGATCGGGGCCCAGAACGCCCCTTGGCAAGGCCTGGCGCTTCCGCGATGCCCAGAGGGTGCTTGGGGGGATGGAGAGAGGGGCGCCCGCCGGGGGAGTTCCGGGAGCCTCGGTGCCTCCCGCCGCAGCTGCAGCGTTCCTCCCGGGAGGCGGCCCAGCCCTTCATCCTCGCCGCCTGAGCTTCTCCGAGGGGGGCTGCAGCCTTGCGGCCGTTGCCACCGCCTGGAGAAGCGGCCCACGCGGACTGA N . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4687235;STD_quant_start=0.000000;STD_quant_stop=0.000000;Kurtosis_quant_start=-1.322564;Kurtosis_quant_stop=1.044626;SVTYPE=DEL;SUPTYPE=AL;SVLEN=-697;STRANDS=+-;STRANDS2=10,15,10,15;RE=25;REF_strand=117632,111071;Strandbias_pval=0.317831;AF=0.000109312 GT:DR:DV 0/0:228678:25 +chr20 4686550 34 AGCCGCGGGGGCCGAGT N . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4686571;STD_quant_start=6.833333;STD_quant_stop=5.657673;Kurtosis_quant_start=-0.182705;Kurtosis_quant_stop=-1.128736;SVTYPE=DEL;SUPTYPE=AL;SVLEN=-21;STRANDS=+-;STRANDS2=241,191,241,191;RE=432;REF_strand=118716,110155;Strandbias_pval=0.111676;AF=0.00188753 GT:DR:DV 0/0:228439:432 +chr20 4686602 35 GGGTGCCCGGCC N . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4686614;STD_quant_start=5.735312;STD_quant_stop=6.525647;Kurtosis_quant_start=-1.777410;Kurtosis_quant_stop=-1.356973;SVTYPE=DEL;SUPTYPE=AL;SVLEN=-12;STRANDS=+-;STRANDS2=103,123,103,123;RE=226;REF_strand=118581,110359;Strandbias_pval=0.0624802;AF=0.000987158 GT:DR:DV 0/0:228714:226 +chr20 4686637 36 GGAGGGGCCGGG N . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4686653;STD_quant_start=6.633250;STD_quant_stop=7.378294;Kurtosis_quant_start=-1.352271;Kurtosis_quant_stop=-1.431976;SVTYPE=DEL;SUPTYPE=AL;SVLEN=-16;STRANDS=+-;STRANDS2=239,272,239,272;RE=511;REF_strand=118476,110533;Strandbias_pval=0.0266438;AF=0.00223135 GT:DR:DV 0/0:228498:511 +chr20 4686712 37 GAGGCGGCTTGGCTTCGCTTTTCAGGTTAGGAAAGCTCCCTTTACTGCGCGTTGGGGGGCTGGGGGAGCTGGCGGAGCCCCGTTAGGGA N . PASS IMPRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4686809;STD_quant_start=18.923530;STD_quant_stop=16.112107;Kurtosis_quant_start=-0.488129;Kurtosis_quant_stop=-0.202554;SVTYPE=DEL;SUPTYPE=AL;SVLEN=-97;STRANDS=+-;STRANDS2=5,6,5,6;RE=11;REF_strand=118036,110876;Strandbias_pval=0.768489;AF=4.80534e-05 GT:DR:DV 0/0:228901:11 +chr20 4686720 38 TTAGGAAAGCTCCCTTTACTGC N . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4686754;STD_quant_start=9.996153;STD_quant_stop=5.324111;Kurtosis_quant_start=-1.992079;Kurtosis_quant_stop=-1.638936;SVTYPE=DEL;SUPTYPE=AL;SVLEN=-34;STRANDS=+-;STRANDS2=46,59,46,59;RE=105;REF_strand=118116,110799;Strandbias_pval=0.118459;AF=0.000458686 GT:DR:DV 0/0:228810:105 +chr20 4686730 39 N TTTAAGGCTGCACAATACACTACGCAAAGAGC . PASS IMPRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4686753;STD_quant_start=9.398581;STD_quant_stop=15.299237;Kurtosis_quant_start=-1.686003;Kurtosis_quant_stop=-2.085424;SVTYPE=INS;SUPTYPE=AL;SVLEN=11;STRANDS=+-;STRANDS2=18,12,18,12;RE=30;REF_strand=118101,110808;Strandbias_pval=0.368896;AF=0.000131056 GT:DR:DV 0/0:228879:30 +chr20 4686839 40 ACCCCGCGCGGGTCCGGCCCAGCGGGCGATCGCTGGCGCCCAGGGAACTCCGGGAGGGCCGCCAGCGGGCTCCGCAGGGCG N . PASS IMPRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4686917;STD_quant_start=8.099383;STD_quant_stop=16.034338;Kurtosis_quant_start=-1.690320;Kurtosis_quant_stop=-1.758587;SVTYPE=DEL;SUPTYPE=AL;SVLEN=-78;STRANDS=+-;STRANDS2=11,6,11,6;RE=17;REF_strand=117574,111251;Strandbias_pval=0.335459;AF=7.42926e-05 GT:DR:DV 0/0:228808:17 +chr20 4686928 41 CGCGGGGCTCGCGCTCCCCGCCCGTTG N . STRANDBIAS IMPRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4686971;STD_quant_start=8.552795;STD_quant_stop=16.292947;Kurtosis_quant_start=-1.680287;Kurtosis_quant_stop=-1.722140;SVTYPE=DEL;SUPTYPE=AL;SVLEN=-43;STRANDS=+-;STRANDS2=257,396,257,396;RE=653;REF_strand=117317,111462;Strandbias_pval=1.32216e-09;AF=0.00285428 GT:DR:DV 0/0:228126:653 +chr20 4686937 42 N GAAGGCGCGCTGGCGCTGCTGGG . STRANDBIAS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4686947;STD_quant_start=9.390233;STD_quant_stop=9.499226;Kurtosis_quant_start=-1.984728;Kurtosis_quant_stop=-1.791441;SVTYPE=INS;SUPTYPE=AL;SVLEN=12;STRANDS=+-;STRANDS2=29,5,29,5;RE=34;REF_strand=117349,111423;Strandbias_pval=4.59885e-05;AF=0.00014862 GT:DR:DV 0/0:228738:34 +chr20 4686997 43 CAGAACGCCCCTTG N . STRANDBIAS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4687018;STD_quant_start=6.530697;STD_quant_stop=8.734987;Kurtosis_quant_start=-1.907811;Kurtosis_quant_stop=-1.916405;SVTYPE=DEL;SUPTYPE=AL;SVLEN=-21;STRANDS=+-;STRANDS2=40,1,40,1;RE=41;REF_strand=117148,111661;Strandbias_pval=5.56379e-11;AF=0.000179189 GT:DR:DV 0/0:228768:41 +chr20 4687066 44 GGGGCGCCCGCCGGGGGAGTTC N . STRANDBIAS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4687084;STD_quant_start=3.187246;STD_quant_stop=4.855221;Kurtosis_quant_start=0.584628;Kurtosis_quant_stop=-1.610021;SVTYPE=DEL;SUPTYPE=AL,NR;SVLEN=-18;STRANDS=+-;STRANDS2=64,100,64,100;RE=164;REF_strand=116927,111884;Strandbias_pval=0.00222621;AF=0.000716749 GT:DR:DV 0/0:228647:164 +chr20 4687051 45 N GGGGGGGGGGG . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4687051;STD_quant_start=1.612452;STD_quant_stop=3.055050;Kurtosis_quant_start=-0.633639;Kurtosis_quant_stop=-0.193673;SVTYPE=INS;SUPTYPE=AL;SVLEN=11;STRANDS=+-;STRANDS2=20,11,20,11;RE=31;REF_strand=117008,111816;Strandbias_pval=0.15284;AF=0.000135475 GT:DR:DV 0/0:228793:31 +chr20 4687171 46 CGAGGGGGGCTG N . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4687185;STD_quant_start=2.973568;STD_quant_stop=2.982405;Kurtosis_quant_start=-0.334366;Kurtosis_quant_stop=-0.378894;SVTYPE=DEL;SUPTYPE=AL,NR;SVLEN=-14;STRANDS=+-;STRANDS2=17,21,17,21;RE=38;REF_strand=116628,112082;Strandbias_pval=0.517144;AF=0.000166149 GT:DR:DV 0/0:228672:38 +chr20 4687180 47 CGAGGGGGGCTGCAGCCTTGCGGCCGTTGCCACCGCCTGGAGAAGCGGCCCACGCGGACTGACGGGCGGGGGCGGGGCCTCGGGCCTCGGCGGGGGCGGGGTCCGGGGAGGCCCCACCCTCTGTTCTCCAGGGGCGGGGAGAGAGGAGCTGCAGGTCTGCGGCCT N . PASS IMPRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4687331;STD_quant_start=29.072324;STD_quant_stop=23.918612;Kurtosis_quant_start=0.079161;Kurtosis_quant_stop=-1.025238;SVTYPE=DEL;SUPTYPE=AL;SVLEN=-151;STRANDS=+-;STRANDS2=6,4,6,4;RE=10;REF_strand=116384,112082;Strandbias_pval=0.754337;AF=4.37702e-05 GT:DR:DV 0/0:228456:10 +chr20 4687175 48 CCACCGCCTGGAGAAGCGGCCCACGCGGAC N . STRANDBIAS IMPRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4687231;STD_quant_start=10.860609;STD_quant_stop=9.646096;Kurtosis_quant_start=-1.491624;Kurtosis_quant_stop=-2.004481;SVTYPE=DEL;SUPTYPE=AL,NR;SVLEN=-56;STRANDS=+-;STRANDS2=131,82,131,82;RE=213;REF_strand=116556,112083;Strandbias_pval=0.00247554;AF=0.0009316 GT:DR:DV 0/0:228426:213 +chr20 4687263 49 CGGGGGCGGGGTC N . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4687276;STD_quant_start=5.591299;STD_quant_stop=5.450419;Kurtosis_quant_start=-1.764821;Kurtosis_quant_stop=-1.661855;SVTYPE=DEL;SUPTYPE=AL,NR;SVLEN=-13;STRANDS=+-;STRANDS2=177,219,177,219;RE=396;REF_strand=116343,112084;Strandbias_pval=0.0136668;AF=0.0017336 GT:DR:DV 0/0:228031:396 +chr20 4687345 50 GGTGCGATGGC N . STRANDBIAS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4687356;STD_quant_start=3.610330;STD_quant_stop=4.268974;Kurtosis_quant_start=-0.694202;Kurtosis_quant_stop=1.122466;SVTYPE=DEL;SUPTYPE=AL;SVLEN=-11;STRANDS=+-;STRANDS2=79,38,79,38;RE=117;REF_strand=116084,112082;Strandbias_pval=0.000393979;AF=0.000512785 GT:DR:DV 0/0:228049:117 +chr20 4687452 51 CCCTTGGGTCACCGGTCTCC N . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4687472;STD_quant_start=3.660601;STD_quant_stop=2.049390;Kurtosis_quant_start=-0.932822;Kurtosis_quant_stop=1.081466;SVTYPE=DEL;SUPTYPE=AL;SVLEN=-20;STRANDS=+-;STRANDS2=14,5,14,5;RE=19;REF_strand=115779,112080;Strandbias_pval=0.0642151;AF=8.33849e-05 GT:DR:DV 0/0:227840:19 +chr20 4687579 52 ATTTTTTTTTTAA N . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4687602;STD_quant_start=7.108605;STD_quant_stop=6.510537;Kurtosis_quant_start=-1.695016;Kurtosis_quant_stop=-1.737028;SVTYPE=DEL;SUPTYPE=AL;SVLEN=-23;STRANDS=+-;STRANDS2=64,60,64,60;RE=124;REF_strand=115381,112080;Strandbias_pval=0.857877;AF=0.000545148 GT:DR:DV 0/0:227337:124 +chr20 4687590 53 N TTTTTTTTTTTTTTTTTTTTTTTTTGTTTTTTTTTTTTTTTT . STRANDBIAS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4687590;STD_quant_start=0.000000;STD_quant_stop=2.151257;Kurtosis_quant_start=-0.477242;Kurtosis_quant_stop=-0.872008;SVTYPE=INS;SUPTYPE=AL;SVLEN=11;STRANDS=+-;STRANDS2=76,11,76,11;RE=87;REF_strand=115362,112080;Strandbias_pval=1.06505e-12;AF=0.000382515 GT:DR:DV 0/0:227355:87 +chr20 4687660 54 N TTTTTTTTTTTTTTTTTTTTTTTTTT . PASS IMPRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4687666;STD_quant_start=9.433981;STD_quant_stop=10.163661;Kurtosis_quant_start=-1.315059;Kurtosis_quant_stop=-1.723025;SVTYPE=INS;SUPTYPE=AL;SVLEN=19;STRANDS=+-;STRANDS2=9,6,9,6;RE=15;REF_strand=115208,112079;Strandbias_pval=0.607748;AF=6.59959e-05 GT:DR:DV 0/0:227272:15 +chr20 4687733 55 ATGGCCGCGTTATTTTCTTGTTCTG N . STRANDBIAS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4687766;STD_quant_start=4.672615;STD_quant_stop=6.137318;Kurtosis_quant_start=0.130462;Kurtosis_quant_stop=-0.451763;SVTYPE=DEL;SUPTYPE=AL;SVLEN=-33;STRANDS=+-;STRANDS2=29,7,29,7;RE=36;REF_strand=114997,112076;Strandbias_pval=0.000324698;AF=0.000158539 GT:DR:DV 0/0:227037:36 +chr20 4687768 56 N AAAAAAAAAAAAA . PASS IMPRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4687824;STD_quant_start=17.742307;STD_quant_stop=19.420553;Kurtosis_quant_start=-2.068560;Kurtosis_quant_stop=-2.208914;SVTYPE=INS;SUPTYPE=AL;SVLEN=11;STRANDS=+-;STRANDS2=27,12,27,12;RE=39;REF_strand=114874,112073;Strandbias_pval=0.0241051;AF=0.000171846 GT:DR:DV 0/0:226908:39 +chr20 4687867 57 N GGAAAGCAAGGGACAACAGAGGCATACAATAGAA . PASS IMPRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4687913;STD_quant_start=22.961506;STD_quant_stop=8.744229;Kurtosis_quant_start=-2.105004;Kurtosis_quant_stop=-2.016046;SVTYPE=INS;SUPTYPE=AL;SVLEN=11;STRANDS=+-;STRANDS2=8,19,8,19;RE=27;REF_strand=114580,112065;Strandbias_pval=0.033965;AF=0.000119129 GT:DR:DV 0/0:226618:27 +chr20 4687972 58 N . PASS IMPRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4688028;STD_quant_start=7.522294;STD_quant_stop=19.938112;Kurtosis_quant_start=-1.581288;Kurtosis_quant_stop=-2.164052;SVTYPE=DEL;SUPTYPE=AL;SVLEN=-56;STRANDS=+-;STRANDS2=64,43,64,43;RE=107;REF_strand=113645,111584;Strandbias_pval=0.0536897;AF=0.000475072 GT:DR:DV 0/0:225122:107 +chr20 28641496 59 GCCCAGGACAGCTTTGAATGCA N . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=28641518;STD_quant_start=0.000000;STD_quant_stop=0.000000;Kurtosis_quant_start=0.734694;Kurtosis_quant_stop=-0.801799;SVTYPE=DEL;SUPTYPE=AL;SVLEN=-22;STRANDS=+-;STRANDS2=7,18,7,18;RE=25;REF_strand=14,40;Strandbias_pval=1;AF=0.462963 GT:DR:DV 0/1:29:25 +chr20 29408712 60 N TCTCCTTCCGTTTCTA . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=29408712;STD_quant_start=2.529822;STD_quant_stop=2.569047;Kurtosis_quant_start=-1.000000;Kurtosis_quant_stop=-1.307555;SVTYPE=INS;SUPTYPE=AL;SVLEN=18;STRANDS=+-;STRANDS2=6,5,6,5;RE=11;REF_strand=16,10;Strandbias_pval=0.727726;AF=0.423077 GT:DR:DV 0/1:15:11 diff --git a/SVs_sniffles/vcf/55050_bodySnif.vcf b/SVs_sniffles/vcf/55050_bodySnif.vcf new file mode 100644 index 0000000..55ef927 --- /dev/null +++ b/SVs_sniffles/vcf/55050_bodySnif.vcf @@ -0,0 +1,36 @@ +##fileformat=VCFv4.1 +##source=Sniffles +##fileDate=20210810:56:30 AMef_minus +##contig= +##ALT= +##ALT= +##ALT= +##ALT= +##ALT= +##ALT= +##FILTER= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##FORMAT= +##FORMAT= +##FORMAT= +#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT bamfilt/55050_f.bam diff --git a/SVs_sniffles/vcf/55050_promoterSnif.vcf b/SVs_sniffles/vcf/55050_promoterSnif.vcf new file mode 100644 index 0000000..0b0ce76 --- /dev/null +++ b/SVs_sniffles/vcf/55050_promoterSnif.vcf @@ -0,0 +1,98 @@ +##fileformat=VCFv4.1 +##source=Sniffles +##fileDate=20210811:42:30 AMef_minus +##contig= +##ALT= +##ALT= +##ALT= +##ALT= +##ALT= +##ALT= +##FILTER= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##FORMAT= +##FORMAT= +##FORMAT= +#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT promoterbamfilt/55050_f.bam +chr20 2823634 0 CCGGCTGCCATCCCATCTAGGAAGTGAGGAGCGTCTCTG N . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=2823673;STD_quant_start=3.478505;STD_quant_stop=4.012481;Kurtosis_quant_start=0.869271;Kurtosis_quant_stop=-0.197253;SVTYPE=DEL;SUPTYPE=AL;SVLEN=-39;STRANDS=+-;STRANDS2=7,3,7,3;RE=10;REF_strand=14,6;Strandbias_pval=1;AF=0.5 GT:DR:DV 0/1:10:10 +chr20 4685224 1 N TTTTTTTTTTTTTTT . STRANDBIAS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4685224;STD_quant_start=0.000000;STD_quant_stop=0.809379;Kurtosis_quant_start=74.394896;Kurtosis_quant_stop=6.382532;SVTYPE=INS;SUPTYPE=AL;SVLEN=11;STRANDS=+-;STRANDS2=2559,91,2559,91;RE=2650;REF_strand=97642,100784;Strandbias_pval=0;AF=0.0133551 GT:DR:DV 0/0:195776:2650 +chr20 4685224 2 TTTTTTTTTTTTTT N . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4685235;STD_quant_start=0.000000;STD_quant_stop=1.546620;Kurtosis_quant_start=1.785101;Kurtosis_quant_stop=0.968912;SVTYPE=DEL;SUPTYPE=AL,NR;SVLEN=-11;STRANDS=+-;STRANDS2=440,515,440,515;RE=955;REF_strand=97645,100815;Strandbias_pval=0.0555962;AF=0.00481205 GT:DR:DV 0/0:197505:955 +chr20 4685224 3 N TTTTTTTTTTTTTTTTTTTTTTTTTTT . STRANDBIAS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4685224;STD_quant_start=0.000000;STD_quant_stop=1.911573;Kurtosis_quant_start=14.776292;Kurtosis_quant_stop=1.806869;SVTYPE=INS;SUPTYPE=AL;SVLEN=17;STRANDS=+-;STRANDS2=553,31,553,31;RE=584;REF_strand=97642,100784;Strandbias_pval=3.55456e-128;AF=0.00294316 GT:DR:DV 0/0:197842:584 +chr20 4685245 4 GAGACAAAGAGT N . STRANDBIAS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4685257;STD_quant_start=2.270208;STD_quant_stop=2.320477;Kurtosis_quant_start=0.073626;Kurtosis_quant_stop=-0.801695;SVTYPE=DEL;SUPTYPE=AL,NR;SVLEN=-12;STRANDS=+-;STRANDS2=4,22,4,22;RE=26;REF_strand=97652,100926;Strandbias_pval=0.000556094;AF=0.000130931 GT:DR:DV 0/0:198552:26 +chr20 4685314 5 N AAAAAAAAAAAA . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4685321;STD_quant_start=8.420214;STD_quant_stop=7.713624;Kurtosis_quant_start=-1.173145;Kurtosis_quant_stop=-1.488166;SVTYPE=INS;SUPTYPE=AL;SVLEN=11;STRANDS=+-;STRANDS2=13,5,13,5;RE=18;REF_strand=97776,101332;Strandbias_pval=0.059601;AF=9.04032e-05 GT:DR:DV 0/0:199090:18 +chr20 4685356 6 CCCATCTCAGCCTC N . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4685370;STD_quant_start=7.366317;STD_quant_stop=7.438638;Kurtosis_quant_start=-1.663260;Kurtosis_quant_stop=-1.761688;SVTYPE=DEL;SUPTYPE=AL;SVLEN=-14;STRANDS=+-;STRANDS2=105,94,105,94;RE=199;REF_strand=97779,101526;Strandbias_pval=0.320746;AF=0.00099847 GT:DR:DV 0/0:199106:199 +chr20 4685413 7 TTTTTTTTATT N . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4685424;STD_quant_start=2.563480;STD_quant_stop=3.860669;Kurtosis_quant_start=-0.890077;Kurtosis_quant_stop=0.231400;SVTYPE=DEL;SUPTYPE=AL;SVLEN=-11;STRANDS=+-;STRANDS2=25,18,25,18;RE=43;REF_strand=97784,101735;Strandbias_pval=0.285605;AF=0.000215518 GT:DR:DV 0/0:199476:43 +chr20 4685413 8 N TTTTTTTTTTTT . STRANDBIAS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4685414;STD_quant_start=0.000000;STD_quant_stop=5.444263;Kurtosis_quant_start=1.230704;Kurtosis_quant_stop=-0.498250;SVTYPE=INS;SUPTYPE=AL;SVLEN=11;STRANDS=+-;STRANDS2=87,13,87,13;RE=100;REF_strand=97784,101713;Strandbias_pval=2.06889e-15;AF=0.000501261 GT:DR:DV 0/0:199397:100 +chr20 4685435 9 TGGGGTCTCAC N . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4685446;STD_quant_start=5.220767;STD_quant_stop=5.879124;Kurtosis_quant_start=-1.605082;Kurtosis_quant_stop=-1.533703;SVTYPE=DEL;SUPTYPE=AL;SVLEN=-11;STRANDS=+-;STRANDS2=40,39,40,39;RE=79;REF_strand=97784,101842;Strandbias_pval=0.822228;AF=0.00039574 GT:DR:DV 0/0:199547:79 +chr20 4685597 10 N AAAAAAAAAAAAAAAAAAAAAAAAAA . STRANDBIAS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4685606;STD_quant_start=8.104580;STD_quant_stop=8.130514;Kurtosis_quant_start=-1.131785;Kurtosis_quant_stop=-1.691735;SVTYPE=INS;SUPTYPE=AL;SVLEN=11;STRANDS=+-;STRANDS2=10,28,10,28;RE=38;REF_strand=97786,102355;Strandbias_pval=0.00552659;AF=0.000189866 GT:DR:DV 0/0:200103:38 +chr20 4685636 11 GCCTGGTTTAC N . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4685647;STD_quant_start=4.361192;STD_quant_stop=4.113393;Kurtosis_quant_start=-1.728409;Kurtosis_quant_stop=-1.500798;SVTYPE=DEL;SUPTYPE=AL;SVLEN=-11;STRANDS=+-;STRANDS2=56,45,56,45;RE=101;REF_strand=97788,102486;Strandbias_pval=0.196211;AF=0.000504309 GT:DR:DV 0/0:200173:101 +chr20 4685689 12 TAAGATCCCCCTCCCTC N . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4685706;STD_quant_start=2.523225;STD_quant_stop=2.250926;Kurtosis_quant_start=-0.465775;Kurtosis_quant_stop=-0.784735;SVTYPE=DEL;SUPTYPE=AL;SVLEN=-17;STRANDS=+-;STRANDS2=32,29,32,29;RE=61;REF_strand=97788,102676;Strandbias_pval=0.609462;AF=0.000304294 GT:DR:DV 0/0:200403:61 +chr20 4685777 13 GCAAGAACACA N . STRANDBIAS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4685789;STD_quant_start=2.749331;STD_quant_stop=4.835530;Kurtosis_quant_start=-0.131288;Kurtosis_quant_stop=-0.714923;SVTYPE=DEL;SUPTYPE=AL;SVLEN=-12;STRANDS=+-;STRANDS2=59,9,59,9;RE=68;REF_strand=97790,102930;Strandbias_pval=6.73022e-11;AF=0.00033878 GT:DR:DV 0/0:200652:68 +chr20 4685835 14 N TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT . STRANDBIAS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4685840;STD_quant_start=0.000000;STD_quant_stop=5.041494;Kurtosis_quant_start=-1.364068;Kurtosis_quant_stop=-1.882909;SVTYPE=INS;SUPTYPE=AL;SVLEN=15;STRANDS=+-;STRANDS2=22,3,22,3;RE=25;REF_strand=97791,103125;Strandbias_pval=6.3407e-05;AF=0.00012443 GT:DR:DV 0/0:200891:25 +chr20 4685915 15 GGAAGGAACAGGTGATGGT N . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4685941;STD_quant_start=7.764388;STD_quant_stop=7.314813;Kurtosis_quant_start=-1.731096;Kurtosis_quant_stop=-1.610123;SVTYPE=DEL;SUPTYPE=AL;SVLEN=-26;STRANDS=+-;STRANDS2=66,89,66,89;RE=155;REF_strand=97785,103383;Strandbias_pval=0.147831;AF=0.0007705 GT:DR:DV 0/0:201013:155 +chr20 4685896 16 N GGGGGAAGAAGA . PASS IMPRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4685919;STD_quant_start=10.830512;STD_quant_stop=11.916375;Kurtosis_quant_start=-1.578577;Kurtosis_quant_stop=-1.670974;SVTYPE=INS;SUPTYPE=AL;SVLEN=20;STRANDS=+-;STRANDS2=8,8,8,8;RE=16;REF_strand=97791,103313;Strandbias_pval=1;AF=7.95608e-05 GT:DR:DV 0/0:201088:16 +chr20 4685959 17 TCAAAATTTAAGAG N . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4685973;STD_quant_start=3.130495;STD_quant_stop=4.024922;Kurtosis_quant_start=0.013998;Kurtosis_quant_stop=1.834650;SVTYPE=DEL;SUPTYPE=AL;SVLEN=-14;STRANDS=+-;STRANDS2=9,6,9,6;RE=15;REF_strand=97738,103522;Strandbias_pval=0.444023;AF=7.45305e-05 GT:DR:DV 0/0:201245:15 +chr20 4685966 18 N AAAGAAAAAGA . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4685969;STD_quant_start=4.415880;STD_quant_stop=5.449771;Kurtosis_quant_start=-1.468277;Kurtosis_quant_stop=-1.459719;SVTYPE=INS;SUPTYPE=AL;SVLEN=11;STRANDS=+-;STRANDS2=11,7,11,7;RE=18;REF_strand=97732,103520;Strandbias_pval=0.348777;AF=8.94401e-05 GT:DR:DV 0/0:201234:18 +chr20 4686020 19 N AAAAAAAAAAAAAAAAAAA . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4686025;STD_quant_start=6.723095;STD_quant_stop=6.379655;Kurtosis_quant_start=0.128446;Kurtosis_quant_stop=-0.924063;SVTYPE=INS;SUPTYPE=AL;SVLEN=17;STRANDS=+-;STRANDS2=8,4,8,4;RE=12;REF_strand=97529,103706;Strandbias_pval=0.254545;AF=5.96318e-05 GT:DR:DV 0/0:201223:12 +chr20 4686075 20 CCTCATTCCTGAG N . STRANDBIAS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4686088;STD_quant_start=2.150105;STD_quant_stop=2.522034;Kurtosis_quant_start=-0.300011;Kurtosis_quant_stop=0.977779;SVTYPE=DEL;SUPTYPE=AL;SVLEN=-13;STRANDS=+-;STRANDS2=94,29,94,29;RE=123;REF_strand=97301,103906;Strandbias_pval=2.9068e-10;AF=0.000611311 GT:DR:DV 0/0:201084:123 +chr20 4686121 21 GGGGAGCTGGAGCTTTGGGCCGAAT N . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4686142;STD_quant_start=4.954899;STD_quant_stop=4.485805;Kurtosis_quant_start=-1.816674;Kurtosis_quant_stop=-0.604048;SVTYPE=DEL;SUPTYPE=AL,NR;SVLEN=-21;STRANDS=+-;STRANDS2=41,57,41,57;RE=98;REF_strand=97077,104059;Strandbias_pval=0.225295;AF=0.000487233 GT:DR:DV 0/0:201038:98 +chr20 4686167 22 N ACACACACACACAC . STRANDBIAS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4686172;STD_quant_start=5.932959;STD_quant_stop=7.661593;Kurtosis_quant_start=-1.554189;Kurtosis_quant_stop=-1.308619;SVTYPE=INS;SUPTYPE=AL;SVLEN=11;STRANDS=+-;STRANDS2=16,4,16,4;RE=20;REF_strand=96912,104185;Strandbias_pval=0.00584818;AF=9.94545e-05 GT:DR:DV 0/0:201077:20 +chr20 4686244 23 TTTTTCCGGTGAC N . STRANDBIAS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4686263;STD_quant_start=5.108816;STD_quant_stop=4.159327;Kurtosis_quant_start=-0.190704;Kurtosis_quant_stop=-0.508350;SVTYPE=DEL;SUPTYPE=AL;SVLEN=-19;STRANDS=+-;STRANDS2=14,2,14,2;RE=16;REF_strand=96509,104474;Strandbias_pval=0.00171836;AF=7.96087e-05 GT:DR:DV 0/0:200967:16 +chr20 4686249 24 N TTTTTTTTTTTTTTTTTTTTTTTTTGTTTTTTTTTTTTTTTTTTTT . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4686254;STD_quant_start=3.507136;STD_quant_stop=8.191459;Kurtosis_quant_start=0.445613;Kurtosis_quant_stop=-0.563524;SVTYPE=INS;SUPTYPE=AL;SVLEN=11;STRANDS=+-;STRANDS2=9,5,9,5;RE=14;REF_strand=96515,104467;Strandbias_pval=0.287489;AF=6.9658e-05 GT:DR:DV 0/0:200968:14 +chr20 4686326 25 GGGGGCACAGAGTGTGCGCCGGGCCGCGCGGCAATTGGTCCCCGCGCCGACCTCCGCCCGCGAGCGCCGCCGCTTCCCTTCCCCGCCCCGCGTCCCTCCCCCTCGGCCCCGCGCGTCGCCTGTCCTCCGAGCCAGTCGCTGACAGCCGCGGCGCCGCGAGCTTCTCCTCTCCTCACGACCGAGGCAGGTAAACGCCCGGGGTGGGAGGAACGCGGGCGGGGGCAGGGGAGCCGCGGGGGCCGAGTGAGGACCCCGGGCCTCGGGTCCCAGGCGCAAGGGTGCCCGGCCGGGCGGGGTCGGGACCCCAGTGAGGAGGGGCCGGGGGCTGCCCCGCGGGCGCGTGACGCGTCTCGGGCCTGCCCGGCTGCGCTGGTCTCCGCTCGGGTGAGGCGGCTTGGCTTCGCTTTTCAGGTTAGGAAAGCTCCCTTTACTGCGCGTTGGGGGGCTGGGGGAGCTGGCGGAGCCCCGTTAGGGAGGTCGGTGGCGCCGGGGTGTCTCAGCGCCCCCTGCACCCCGCGCGGGTCCGGCCCAGCGGGCGATCGCTGGCGCCCAGGGAACTCCGGGAGGGCCGCCAGCGGGCTCCGCAGGGCGCGGGGCGGGGAGGGGCGCCTGGGGGCCGCGGGGCTCGCGCTCCCCGCCCGTTGGCCGCCCCTCGGAGGCCGAGATCGGGGCCCAGAACGCCCCTTGGCAAGGCCTGGCGCTTCCGCGATGCCCAGAGGGTGCTTGGGGGGATGGAGAGAGGGGCGCCCGCCG N . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4687079;STD_quant_start=0.000000;STD_quant_stop=0.229416;Kurtosis_quant_start=-1.004802;Kurtosis_quant_stop=0.805238;SVTYPE=DEL;SUPTYPE=AL;SVLEN=-753;STRANDS=+-;STRANDS2=18,21,18,21;RE=39;REF_strand=94824,106039;Strandbias_pval=1;AF=0.000194162 GT:DR:DV 0/0:200824:39 +chr20 4686337 26 GTGTGCGCCGGGCCGC N . STRANDBIAS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4686353;STD_quant_start=4.423201;STD_quant_stop=4.551664;Kurtosis_quant_start=-0.966089;Kurtosis_quant_stop=-0.275778;SVTYPE=DEL;SUPTYPE=AL,NR;SVLEN=-16;STRANDS=+-;STRANDS2=36,135,36,135;RE=171;REF_strand=96049,104699;Strandbias_pval=5.17782e-13;AF=0.000851814 GT:DR:DV 0/0:200577:171 +chr20 4686411 27 CCCCGCGTCCCT N . STRANDBIAS IMPRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4686437;STD_quant_start=10.944639;STD_quant_stop=14.551135;Kurtosis_quant_start=-1.778854;Kurtosis_quant_stop=-1.905274;SVTYPE=DEL;SUPTYPE=AL,NR;SVLEN=-26;STRANDS=+-;STRANDS2=186,299,186,299;RE=485;REF_strand=95689,104913;Strandbias_pval=4.01081e-05;AF=0.00241772 GT:DR:DV 0/0:200117:485 +chr20 4686486 28 CTTCTCCTCTC N . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4686497;STD_quant_start=3.096214;STD_quant_stop=2.717465;Kurtosis_quant_start=-1.091412;Kurtosis_quant_stop=-0.522945;SVTYPE=DEL;SUPTYPE=AL,NR;SVLEN=-11;STRANDS=+-;STRANDS2=91,118,91,118;RE=209;REF_strand=95412,105104;Strandbias_pval=0.267575;AF=0.00104231 GT:DR:DV 0/0:200307:209 +chr20 4686456 29 N CCCTGGCGTCGTGCGTCGCGCGCGCGT . PASS IMPRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4686466;STD_quant_start=8.031189;STD_quant_stop=11.857487;Kurtosis_quant_start=-1.611542;Kurtosis_quant_stop=-1.493884;SVTYPE=INS;SUPTYPE=AL;SVLEN=14;STRANDS=+-;STRANDS2=8,9,8,9;RE=17;REF_strand=95539,105016;Strandbias_pval=1;AF=8.47648e-05 GT:DR:DV 0/0:200538:17 +chr20 4686492 30 TCTCCTCTCCTCACGAC N . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4686505;STD_quant_start=3.861229;STD_quant_stop=3.343923;Kurtosis_quant_start=-0.525428;Kurtosis_quant_stop=-0.966640;SVTYPE=DEL;SUPTYPE=AL,NR;SVLEN=-13;STRANDS=+-;STRANDS2=30,15,30,15;RE=45;REF_strand=95391,105123;Strandbias_pval=0.0110323;AF=0.000224423 GT:DR:DV 0/0:200469:45 +chr20 4686538 31 CGGGCGGGGGCAGGGGAGCCGCGGGGGCCGAGTGAGGACCCCGGGCCTCGGGTCCCAGGCGCAAGGGTGCCCGGCCGGGCGGGGTCGGGACCCCAGTGAGGAGGGGCCGGGGGCTGCCCCGCGGGCGCGTGACGCGTCTCGGGCCTGCCCGGCTGCGCTGGTCTCCGCTCGGGTGAGGCGGCTTGGCTTCGCTTTTCAGGTTAGGAAAGCTCCCTTTACTGCGCGTTGGGGGGCTGGGGGAGCTGGCGGAGCCCCGTTAGGGAGGTCGGTGGCGCCGGGGTGTCTCAGCGCCCCCTGCACCCCGCGCGGGTCCGGCCCAGCGGGCGATCGCTGGCGCCCAGGGAACTCCGGGAGGGCCGCCAGCGGGCTCCGCAGGGCGCGGGGCGGGGAGGGGCGCCTGGGGGCCGCGGGGCTCGCGCTCCCCGCCCGTTGGCCGCCCCTCGGAGGCCGAGATCGGGGCCCAGAACGCCCCTTGGCAAGGCCTGGCGCTTCCGCGATGCCCAGAGGGTGCTTGGGGGGATGGAGAGAGGGGCGCCCGCCGGGGGAGTTCCGGGAGCCTCGGTGCCTCCCGCCGCAGCTGCAGCGTTCCTCCCGGGAGGCGGCCCAGCCCTTCATCCTCGCCGCCTGAGCTTCTCCGAGGGGGGCTGCAGCCTTGCGGCCGTTGCCACCGCCTGGAGAAGCGGCCCACGCGGACTGA N . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4687235;STD_quant_start=0.603023;STD_quant_stop=0.797724;Kurtosis_quant_start=0.733313;Kurtosis_quant_stop=0.010306;SVTYPE=DEL;SUPTYPE=AL;SVLEN=-697;STRANDS=+-;STRANDS2=15,7,15,7;RE=22;REF_strand=94190,106437;Strandbias_pval=0.0545507;AF=0.000109656 GT:DR:DV 0/0:200605:22 +chr20 4686539 32 GGGGGCCGAGT N . PASS IMPRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4686571;STD_quant_start=10.847369;STD_quant_stop=8.795291;Kurtosis_quant_start=-1.743448;Kurtosis_quant_stop=-1.739341;SVTYPE=DEL;SUPTYPE=AL,NR;SVLEN=-32;STRANDS=+-;STRANDS2=239,294,239,294;RE=533;REF_strand=95199,105291;Strandbias_pval=0.224336;AF=0.00265849 GT:DR:DV 0/0:199957:533 +chr20 4686637 33 GGAGGGGCCGGGGGCT N . STRANDBIAS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4686653;STD_quant_start=8.449097;STD_quant_stop=8.812226;Kurtosis_quant_start=-1.875462;Kurtosis_quant_stop=-1.915621;SVTYPE=DEL;SUPTYPE=AL,NR;SVLEN=-16;STRANDS=+-;STRANDS2=191,280,191,280;RE=471;REF_strand=94982,105689;Strandbias_pval=0.00356543;AF=0.00234713 GT:DR:DV 0/0:200200:471 +chr20 4686768 34 GGGCTGGGGGA N . STRANDBIAS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4686779;STD_quant_start=3.264694;STD_quant_stop=2.995778;Kurtosis_quant_start=-1.369206;Kurtosis_quant_stop=-1.143462;SVTYPE=DEL;SUPTYPE=AL,NR;SVLEN=-11;STRANDS=+-;STRANDS2=29,129,29,129;RE=158;REF_strand=94501,106194;Strandbias_pval=7.39711e-14;AF=0.000787264 GT:DR:DV 0/0:200537:158 +chr20 4686808 35 GGCGCCGGGGTGTCTCAGCGCCCCCTGCACCCCGCGCGGGTCCGGCCCAGCGGGCGATCGCTGGCGCCCAGGGAACTCCGGGAGGGCCGCCAGCGGGCTCCGCAGGGCGCGGGGCGGGGAGGGGCGCCTGGGGGCCGCGGG N . PASS IMPRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4686953;STD_quant_start=13.019217;STD_quant_stop=28.368997;Kurtosis_quant_start=-0.194571;Kurtosis_quant_stop=-0.325111;SVTYPE=DEL;SUPTYPE=AL;SVLEN=-145;STRANDS=+-;STRANDS2=6,5,6,5;RE=11;REF_strand=94151,106612;Strandbias_pval=0.764986;AF=5.4791e-05 GT:DR:DV 0/0:200752:11 +chr20 4686805 36 CCCTGCACCCCG N . STRANDBIAS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4686842;STD_quant_start=8.254551;STD_quant_stop=8.520617;Kurtosis_quant_start=-1.233505;Kurtosis_quant_stop=-1.782416;SVTYPE=DEL;SUPTYPE=AL;SVLEN=-37;STRANDS=+-;STRANDS2=178,259,178,259;RE=437;REF_strand=94339,106385;Strandbias_pval=0.0095056;AF=0.00217712 GT:DR:DV 0/0:200287:437 +chr20 4686877 37 GGCGCCCAGGGAACTCCGGGAGGGCC N . STRANDBIAS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4686896;STD_quant_start=4.190465;STD_quant_stop=4.002499;Kurtosis_quant_start=-1.080751;Kurtosis_quant_stop=-1.471722;SVTYPE=DEL;SUPTYPE=AL;SVLEN=-19;STRANDS=+-;STRANDS2=31,70,31,70;RE=101;REF_strand=94146,106605;Strandbias_pval=0.00129988;AF=0.000503111 GT:DR:DV 0/0:200650:101 +chr20 4686918 38 GGGCGCCTGGGGGCC N . STRANDBIAS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4686944;STD_quant_start=8.540294;STD_quant_stop=6.946475;Kurtosis_quant_start=-1.855424;Kurtosis_quant_stop=-1.590352;SVTYPE=DEL;SUPTYPE=AL;SVLEN=-26;STRANDS=+-;STRANDS2=167,402,167,402;RE=569;REF_strand=93972,106802;Strandbias_pval=2.69595e-17;AF=0.00283403 GT:DR:DV 0/0:200205:569 +chr20 4686968 39 N GGCTTCGCCCCAC . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4686970;STD_quant_start=3.146427;STD_quant_stop=2.626785;Kurtosis_quant_start=-1.160465;Kurtosis_quant_stop=-1.110061;SVTYPE=INS;SUPTYPE=AL;SVLEN=12;STRANDS=+-;STRANDS2=11,9,11,9;RE=20;REF_strand=93852,106984;Strandbias_pval=0.506685;AF=9.95837e-05 GT:DR:DV 0/0:200816:20 +chr20 4686973 40 CGCCCCTCGGAG N . STRANDBIAS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4686984;STD_quant_start=4.037614;STD_quant_stop=3.985439;Kurtosis_quant_start=-1.637913;Kurtosis_quant_stop=-0.554484;SVTYPE=DEL;SUPTYPE=AL;SVLEN=-11;STRANDS=+-;STRANDS2=54,33,54,33;RE=87;REF_strand=93830,107014;Strandbias_pval=0.00495099;AF=0.000433172 GT:DR:DV 0/0:200757:87 +chr20 4687064 41 GAGGGGCGCCCGCCGG N . STRANDBIAS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4687087;STD_quant_start=8.940084;STD_quant_stop=8.353427;Kurtosis_quant_start=-1.472919;Kurtosis_quant_stop=-1.427606;SVTYPE=DEL;SUPTYPE=AL,NR;SVLEN=-23;STRANDS=+-;STRANDS2=154,301,154,301;RE=455;REF_strand=93545,107445;Strandbias_pval=5.35317e-08;AF=0.00226379 GT:DR:DV 0/0:200535:455 +chr20 4687089 42 GGAGCCTCGGT N . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4687101;STD_quant_start=2.039092;STD_quant_stop=4.559548;Kurtosis_quant_start=-1.025558;Kurtosis_quant_stop=-1.071246;SVTYPE=DEL;SUPTYPE=AL;SVLEN=-12;STRANDS=+-;STRANDS2=18,21,18,21;RE=39;REF_strand=93493,107527;Strandbias_pval=1;AF=0.000194011 GT:DR:DV 0/0:200981:39 +chr20 4687123 43 TCCTCCCGGGAGGCGGCCCAGCCCTTCATCCTCGCCGCCTGAGCTTCTCCGAGGGGGGCTGCAGCCTTGCGGCCGTTGCCACCGCCTGGAGAAGCGGCCCACGCGGACTGA N . PASS IMPRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4687236;STD_quant_start=20.734030;STD_quant_stop=23.062957;Kurtosis_quant_start=-0.863440;Kurtosis_quant_stop=1.788704;SVTYPE=DEL;SUPTYPE=AL;SVLEN=-113;STRANDS=+-;STRANDS2=4,6,4,6;RE=10;REF_strand=93277,107643;Strandbias_pval=0.760128;AF=4.97711e-05 GT:DR:DV 0/0:200910:10 +chr20 4687128 44 AGGCGGCCCAGC N . STRANDBIAS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4687146;STD_quant_start=6.618876;STD_quant_stop=8.103497;Kurtosis_quant_start=-1.579784;Kurtosis_quant_stop=-1.802408;SVTYPE=DEL;SUPTYPE=AL;SVLEN=-18;STRANDS=+-;STRANDS2=135,76,135,76;RE=211;REF_strand=93363,107642;Strandbias_pval=3.64519e-07;AF=0.00104973 GT:DR:DV 0/0:200794:211 +chr20 4687139 45 GGCGGCCCAGCCC N . PASS IMPRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4687273;STD_quant_start=28.181554;STD_quant_stop=19.819183;Kurtosis_quant_start=0.235691;Kurtosis_quant_stop=0.200338;SVTYPE=DEL;SUPTYPE=AL;SVLEN=-134;STRANDS=+-;STRANDS2=4,6,4,6;RE=10;REF_strand=93176,107656;Strandbias_pval=0.760232;AF=4.97929e-05 GT:DR:DV 0/0:200822:10 +chr20 4687170 46 N CGCCCCCCTCGAGCAT . PASS IMPRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4687179;STD_quant_start=10.148892;STD_quant_stop=8.413425;Kurtosis_quant_start=-1.963174;Kurtosis_quant_stop=-1.690877;SVTYPE=INS;SUPTYPE=AL;SVLEN=11;STRANDS=+-;STRANDS2=13,16,13,16;RE=29;REF_strand=93274,107666;Strandbias_pval=1;AF=0.000144322 GT:DR:DV 0/0:200911:29 +chr20 4687370 47 GGCCAGTCACATTCCTCC N . STRANDBIAS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4687386;STD_quant_start=5.379285;STD_quant_stop=3.748417;Kurtosis_quant_start=-1.773237;Kurtosis_quant_stop=-0.567840;SVTYPE=DEL;SUPTYPE=AL,NR;SVLEN=-16;STRANDS=+-;STRANDS2=93,66,93,66;RE=159;REF_strand=92736,107668;Strandbias_pval=0.00240325;AF=0.000793397 GT:DR:DV 0/0:200245:159 +chr20 4687590 48 N TTTTTTTTTTT . STRANDBIAS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4687590;STD_quant_start=0.000000;STD_quant_stop=1.754993;Kurtosis_quant_start=1.535963;Kurtosis_quant_stop=-0.407102;SVTYPE=INS;SUPTYPE=AL;SVLEN=11;STRANDS=+-;STRANDS2=42,8,42,8;RE=50;REF_strand=92224,107668;Strandbias_pval=4.0068e-08;AF=0.000250135 GT:DR:DV 0/0:199842:50 +chr20 4687632 49 CTCGCCATCGCAGAGCCACAGCT N . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4687652;STD_quant_start=6.652067;STD_quant_stop=3.667424;Kurtosis_quant_start=-1.030238;Kurtosis_quant_stop=-0.299496;SVTYPE=DEL;SUPTYPE=AL;SVLEN=-20;STRANDS=+-;STRANDS2=20,20,20,20;RE=40;REF_strand=92103,107667;Strandbias_pval=0.6375;AF=0.00020023 GT:DR:DV 0/0:199730:40 +chr20 4687651 50 CGTTTTTGTTTCCTAGCCTCCAGATTCTCACACAACACAGTGCAGTTTCACTGCTGTAATGATGAGGATCTT N . STRANDBIAS IMPRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4687731;STD_quant_start=15.059465;STD_quant_stop=14.672253;Kurtosis_quant_start=-1.909719;Kurtosis_quant_stop=-1.963093;SVTYPE=DEL;SUPTYPE=AL;SVLEN=-80;STRANDS=+-;STRANDS2=57,104,57,104;RE=161;REF_strand=91935,107665;Strandbias_pval=0.00704277;AF=0.000806613 GT:DR:DV 0/0:199439:161 +chr20 4687783 51 CCCATATGATT N . STRANDBIAS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4687794;STD_quant_start=4.316985;STD_quant_stop=3.965763;Kurtosis_quant_start=-1.309687;Kurtosis_quant_stop=-1.618554;SVTYPE=DEL;SUPTYPE=AL;SVLEN=-11;STRANDS=+-;STRANDS2=9,35,9,35;RE=44;REF_strand=91695,107660;Strandbias_pval=0.000687472;AF=0.000220712 GT:DR:DV 0/0:199311:44 +chr20 4687858 52 AAATATAATTATCAAAA N . STRANDBIAS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4687888;STD_quant_start=6.371813;STD_quant_stop=4.788876;Kurtosis_quant_start=-1.278325;Kurtosis_quant_stop=-1.812142;SVTYPE=DEL;SUPTYPE=AL;SVLEN=-30;STRANDS=+-;STRANDS2=5,25,5,25;RE=30;REF_strand=91449,107657;Strandbias_pval=0.00138813;AF=0.000150674 GT:DR:DV 0/0:199076:30 +chr20 4687867 53 N TAAAATAAAGATAAAGAATATAAATATT . STRANDBIAS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4687889;STD_quant_start=8.797727;STD_quant_stop=6.752777;Kurtosis_quant_start=0.710290;Kurtosis_quant_stop=1.778428;SVTYPE=INS;SUPTYPE=AL;SVLEN=13;STRANDS=+-;STRANDS2=1,14,1,14;RE=15;REF_strand=91437,107657;Strandbias_pval=0.00275731;AF=7.53413e-05 GT:DR:DV 0/0:199079:15 +chr20 4687911 54 N AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA . STRANDBIAS IMPRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4687936;STD_quant_start=4.289522;STD_quant_stop=12.473973;Kurtosis_quant_start=-1.498064;Kurtosis_quant_stop=-2.181116;SVTYPE=INS;SUPTYPE=AL;SVLEN=15;STRANDS=+-;STRANDS2=1,17,1,17;RE=18;REF_strand=91310,107652;Strandbias_pval=0.000448343;AF=9.04695e-05 GT:DR:DV 0/0:198944:18 +chr20 4687972 55 N . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4687986;STD_quant_start=6.866696;STD_quant_stop=7.841227;Kurtosis_quant_start=-1.659723;Kurtosis_quant_stop=-1.812192;SVTYPE=DEL;SUPTYPE=AL;SVLEN=-14;STRANDS=+-;STRANDS2=28,39,28,39;RE=67;REF_strand=91061,107623;Strandbias_pval=0.541448;AF=0.000337219 GT:DR:DV 0/0:198617:67 +chr20 4688011 56 N AAAAAAAAAAAAAAAAAAAAAAAAAAAA . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4688011;STD_quant_start=0.000000;STD_quant_stop=3.250000;Kurtosis_quant_start=-0.973116;Kurtosis_quant_stop=-1.339452;SVTYPE=INS;SUPTYPE=AL;SVLEN=11;STRANDS=+-;STRANDS2=8,24,8,24;RE=32;REF_strand=90706,107452;Strandbias_pval=0.0204169;AF=0.000161487 GT:DR:DV 0/0:198126:32 +chr20 28640917 57 N CTTTCTTTCTTTCTTTCTTTCTTTCTTT . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=28640917;STD_quant_start=9.348797;STD_quant_stop=7.771744;Kurtosis_quant_start=-1.745589;Kurtosis_quant_stop=-1.321909;SVTYPE=INS;SUPTYPE=AL;SVLEN=31;STRANDS=+-;STRANDS2=6,10,6,10;RE=16;REF_strand=100,120;Strandbias_pval=0.609917;AF=0.0727273 GT:DR:DV 0/0:204:16 +chr20 28640993 58 N TTTCCTCTTTCTTTCTCT . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=28640993;STD_quant_start=0.000000;STD_quant_stop=0.456435;Kurtosis_quant_start=-0.108177;Kurtosis_quant_stop=-0.571963;SVTYPE=INS;SUPTYPE=AL;SVLEN=18;STRANDS=+-;STRANDS2=25,24,25,24;RE=49;REF_strand=98,120;Strandbias_pval=0.526195;AF=0.224771 GT:DR:DV 0/0:169:49 +chr20 28641063 59 N TCTTTTTCCTTCTCTTC . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=28641067;STD_quant_start=9.823441;STD_quant_stop=5.907622;Kurtosis_quant_start=-1.821744;Kurtosis_quant_stop=0.142306;SVTYPE=INS;SUPTYPE=AL;SVLEN=29;STRANDS=+-;STRANDS2=6,8,6,8;RE=14;REF_strand=96,120;Strandbias_pval=1;AF=0.0648148 GT:DR:DV 0/0:202:14 +chr20 28641136 60 N CTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTT . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=28641136;STD_quant_start=7.742242;STD_quant_stop=7.288030;Kurtosis_quant_start=-1.919965;Kurtosis_quant_stop=-1.809614;SVTYPE=INS;SUPTYPE=AL;SVLEN=36;STRANDS=+-;STRANDS2=47,57,47,57;RE=104;REF_strand=96,122;Strandbias_pval=0.904657;AF=0.477064 GT:DR:DV 0/1:114:104 +chr20 30518453 61 N TAGGACGGAAAGAAGGAAGGAAGGAAGGAAGGAAGGAAAGAAGGAAGGAAGAAGGATGA . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=30518454;STD_quant_start=0.000000;STD_quant_stop=1.671561;Kurtosis_quant_start=0.943065;Kurtosis_quant_stop=0.880423;SVTYPE=INS;SUPTYPE=AL;SVLEN=63;STRANDS=+-;STRANDS2=34,34,34,34;RE=68;REF_strand=68,68;Strandbias_pval=1;AF=0.5 GT:DR:DV 0/1:68:68 diff --git a/SVs_sniffles/vcf/55052_bodySnif.vcf b/SVs_sniffles/vcf/55052_bodySnif.vcf new file mode 100644 index 0000000..e059021 --- /dev/null +++ b/SVs_sniffles/vcf/55052_bodySnif.vcf @@ -0,0 +1,36 @@ +##fileformat=VCFv4.1 +##source=Sniffles +##fileDate=20210810:56:34 AMef_minus +##contig= +##ALT= +##ALT= +##ALT= +##ALT= +##ALT= +##ALT= +##FILTER= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##FORMAT= +##FORMAT= +##FORMAT= +#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT bamfilt/55052_f.bam diff --git a/SVs_sniffles/vcf/55052_promoterSnif.vcf b/SVs_sniffles/vcf/55052_promoterSnif.vcf new file mode 100644 index 0000000..b7d720f --- /dev/null +++ b/SVs_sniffles/vcf/55052_promoterSnif.vcf @@ -0,0 +1,114 @@ +##fileformat=VCFv4.1 +##source=Sniffles +##fileDate=20210811:43:52 AMef_minus +##contig= +##ALT= +##ALT= +##ALT= +##ALT= +##ALT= +##ALT= +##FILTER= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##FORMAT= +##FORMAT= +##FORMAT= +#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT promoterbamfilt/55052_f.bam +chr20 4685115 0 N TCACTGCGACA . STRANDBIAS IMPRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4685122;STD_quant_start=10.681760;STD_quant_stop=12.020815;Kurtosis_quant_start=-0.352276;Kurtosis_quant_stop=-0.437308;SVTYPE=INS;SUPTYPE=AL;SVLEN=14;STRANDS=+-;STRANDS2=11,1,11,1;RE=12;REF_strand=131007,117884;Strandbias_pval=0.00716326;AF=4.82139e-05 GT:DR:DV 0/0:248879:12 +chr20 4685108 1 CTTCTCCTGTCTCTC N . PASS IMPRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4685131;STD_quant_start=9.839264;STD_quant_stop=10.530379;Kurtosis_quant_start=-1.700246;Kurtosis_quant_stop=-1.686969;SVTYPE=DEL;SUPTYPE=AL;SVLEN=-23;STRANDS=+-;STRANDS2=91,89,91,89;RE=180;REF_strand=130999,117866;Strandbias_pval=0.601541;AF=0.000723284 GT:DR:DV 0/0:248685:180 +chr20 4685224 2 TTTTTTTTTTTTTTTT N . STRANDBIAS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4685235;STD_quant_start=0.228048;STD_quant_stop=1.592609;Kurtosis_quant_start=0.567638;Kurtosis_quant_stop=0.227080;SVTYPE=DEL;SUPTYPE=AL,NR;SVLEN=-11;STRANDS=+-;STRANDS2=645,702,645,702;RE=1347;REF_strand=131120,118421;Strandbias_pval=0.000688478;AF=0.00539791 GT:DR:DV 0/0:248194:1347 +chr20 4685224 3 N TTTTTTTTTTT . STRANDBIAS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4685224;STD_quant_start=0.000000;STD_quant_stop=0.992250;Kurtosis_quant_start=119.689567;Kurtosis_quant_stop=4.692846;SVTYPE=INS;SUPTYPE=AL;SVLEN=11;STRANDS=+-;STRANDS2=3255,113,3255,113;RE=3368;REF_strand=131120,118400;Strandbias_pval=0;AF=0.0134979 GT:DR:DV 0/0:246152:3368 +chr20 4685224 4 N TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT . STRANDBIAS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4685224;STD_quant_start=0.000000;STD_quant_stop=2.368869;Kurtosis_quant_start=3.631712;Kurtosis_quant_stop=-0.190687;SVTYPE=INS;SUPTYPE=AL;SVLEN=21;STRANDS=+-;STRANDS2=507,14,507,14;RE=521;REF_strand=131120,118400;Strandbias_pval=1.64642e-119;AF=0.00208801 GT:DR:DV 0/0:248999:521 +chr20 4685240 5 AGAGACAAAGAGTGAGACAGGGTCTTGGCCTATAGCCCTGTGGCC N . PASS IMPRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4685289;STD_quant_start=11.895377;STD_quant_stop=13.217413;Kurtosis_quant_start=-1.228872;Kurtosis_quant_stop=-0.782412;SVTYPE=DEL;SUPTYPE=AL,NR;SVLEN=-49;STRANDS=+-;STRANDS2=3,8,3,8;RE=11;REF_strand=131151,118596;Strandbias_pval=0.130878;AF=4.40446e-05 GT:DR:DV 0/0:249736:11 +chr20 4685304 6 N GGCCAGGCAGGCACA . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4685306;STD_quant_start=7.597847;STD_quant_stop=6.459665;Kurtosis_quant_start=-1.703259;Kurtosis_quant_stop=-1.763654;SVTYPE=INS;SUPTYPE=AL;SVLEN=14;STRANDS=+-;STRANDS2=8,15,8,15;RE=23;REF_strand=131182,118778;Strandbias_pval=0.0980595;AF=9.20147e-05 GT:DR:DV 0/0:249937:23 +chr20 4685356 7 CCCATCTCAGCCTC N . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4685370;STD_quant_start=0.935414;STD_quant_stop=0.763763;Kurtosis_quant_start=-0.063863;Kurtosis_quant_stop=1.665422;SVTYPE=DEL;SUPTYPE=AL;SVLEN=-14;STRANDS=+-;STRANDS2=19,30,19,30;RE=49;REF_strand=131186,118986;Strandbias_pval=0.0628827;AF=0.000195865 GT:DR:DV 0/0:250123:49 +chr20 4685393 8 TGTGCCACCGTTCCCAGCAATTTTTTTT N . STRANDBIAS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4685423;STD_quant_start=7.096423;STD_quant_stop=7.168567;Kurtosis_quant_start=-1.744273;Kurtosis_quant_stop=-1.644889;SVTYPE=DEL;SUPTYPE=AL;SVLEN=-30;STRANDS=+-;STRANDS2=129,78,129,78;RE=207;REF_strand=131186,119111;Strandbias_pval=0.00428451;AF=0.000827018 GT:DR:DV 0/0:250090:207 +chr20 4685413 9 N TTTTTTTTTTT . STRANDBIAS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4685413;STD_quant_start=0.000000;STD_quant_stop=3.608167;Kurtosis_quant_start=1.979553;Kurtosis_quant_stop=-0.685793;SVTYPE=INS;SUPTYPE=AL;SVLEN=11;STRANDS=+-;STRANDS2=96,10,96,10;RE=106;REF_strand=131186,119126;Strandbias_pval=2.90548e-17;AF=0.000423472 GT:DR:DV 0/0:250206:106 +chr20 4685441 10 CTCACTATGTTG N . PASS IMPRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4685494;STD_quant_start=10.052639;STD_quant_stop=10.522463;Kurtosis_quant_start=-1.963511;Kurtosis_quant_stop=-1.995811;SVTYPE=DEL;SUPTYPE=AL,NR;SVLEN=-53;STRANDS=+-;STRANDS2=59,49,59,49;RE=108;REF_strand=131189,119295;Strandbias_pval=0.700157;AF=0.000431165 GT:DR:DV 0/0:250376:108 +chr20 4685413 11 N TTTTTTTTTTTTTTTTTTTTTGC . STRANDBIAS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4685433;STD_quant_start=4.786344;STD_quant_stop=4.748205;Kurtosis_quant_start=-0.130090;Kurtosis_quant_stop=-0.758805;SVTYPE=INS;SUPTYPE=AL;SVLEN=11;STRANDS=+-;STRANDS2=34,10,34,10;RE=44;REF_strand=131186,119162;Strandbias_pval=0.000806441;AF=0.000175755 GT:DR:DV 0/0:250304:44 +chr20 4685493 12 TGCCTTGGCCTCTGAAAG N . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4685504;STD_quant_start=1.781548;STD_quant_stop=3.538607;Kurtosis_quant_start=-1.516064;Kurtosis_quant_stop=-1.815582;SVTYPE=DEL;SUPTYPE=AL;SVLEN=-11;STRANDS=+-;STRANDS2=19,27,19,27;RE=46;REF_strand=131191,119378;Strandbias_pval=0.14196;AF=0.000183582 GT:DR:DV 0/0:250523:46 +chr20 4685584 13 N GCAAAAAAAAAAAA . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4685589;STD_quant_start=4.027082;STD_quant_stop=5.013027;Kurtosis_quant_start=-1.528182;Kurtosis_quant_stop=-1.022936;SVTYPE=INS;SUPTYPE=AL;SVLEN=11;STRANDS=+-;STRANDS2=17,30,17,30;RE=47;REF_strand=131192,119635;Strandbias_pval=0.0286824;AF=0.00018738 GT:DR:DV 0/0:250780:47 +chr20 4685632 14 GTTTACGCCCATTTCACTTTAAAAGTGCCCAATTTGGGTAATAATTTATAAGATCCCCCTCCCTCTAAATCCTGTCCTTCT N . PASS IMPRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4685721;STD_quant_start=7.930952;STD_quant_stop=13.360389;Kurtosis_quant_start=0.427593;Kurtosis_quant_stop=-1.045908;SVTYPE=DEL;SUPTYPE=AL;SVLEN=-89;STRANDS=+-;STRANDS2=9,5,9,5;RE=14;REF_strand=131197,119878;Strandbias_pval=0.430615;AF=5.57602e-05 GT:DR:DV 0/0:251061:14 +chr20 4685695 15 N CCCCCCCCCCC . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4685699;STD_quant_start=7.589466;STD_quant_stop=8.366600;Kurtosis_quant_start=-2.040745;Kurtosis_quant_stop=-1.985870;SVTYPE=INS;SUPTYPE=AL;SVLEN=11;STRANDS=+-;STRANDS2=10,11,10,11;RE=21;REF_strand=131198,119918;Strandbias_pval=0.827764;AF=8.36267e-05 GT:DR:DV 0/0:251095:21 +chr20 4685777 16 GAACACACCAC N . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4685793;STD_quant_start=4.808452;STD_quant_stop=4.886593;Kurtosis_quant_start=-1.532848;Kurtosis_quant_stop=-1.496775;SVTYPE=DEL;SUPTYPE=AL,NR;SVLEN=-16;STRANDS=+-;STRANDS2=79,54,79,54;RE=133;REF_strand=131198,120189;Strandbias_pval=0.0995704;AF=0.000529065 GT:DR:DV 0/0:251254:133 +chr20 4685835 17 N TTTTTTTTTTT . STRANDBIAS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4685837;STD_quant_start=1.433721;STD_quant_stop=5.238745;Kurtosis_quant_start=-1.318531;Kurtosis_quant_stop=-1.776603;SVTYPE=INS;SUPTYPE=AL;SVLEN=11;STRANDS=+-;STRANDS2=30,7,30,7;RE=37;REF_strand=131198,120371;Strandbias_pval=0.000397775;AF=0.000147077 GT:DR:DV 0/0:251532:37 +chr20 4685942 18 AGTGTCCTTTCT N . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4685954;STD_quant_start=5.590170;STD_quant_stop=4.879805;Kurtosis_quant_start=-1.608212;Kurtosis_quant_stop=-1.558165;SVTYPE=DEL;SUPTYPE=AL,NR;SVLEN=-12;STRANDS=+-;STRANDS2=61,36,61,36;RE=97;REF_strand=131178,120662;Strandbias_pval=0.0415099;AF=0.000385165 GT:DR:DV 0/0:251743:97 +chr20 4685966 19 AAGAGTTTATGTGAA N . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4685980;STD_quant_start=4.722288;STD_quant_stop=5.779273;Kurtosis_quant_start=-0.995522;Kurtosis_quant_stop=1.225405;SVTYPE=DEL;SUPTYPE=AL;SVLEN=-14;STRANDS=+-;STRANDS2=8,5,8,5;RE=13;REF_strand=131113,120725;Strandbias_pval=0.585306;AF=5.16205e-05 GT:DR:DV 0/0:251825:13 +chr20 4686021 20 N TTTTTTTTTTTTTTTTT . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4686035;STD_quant_start=2.807553;STD_quant_stop=8.373628;Kurtosis_quant_start=-1.221991;Kurtosis_quant_stop=-1.440275;SVTYPE=INS;SUPTYPE=AL;SVLEN=11;STRANDS=+-;STRANDS2=24,11,24,11;RE=35;REF_strand=130836,120825;Strandbias_pval=0.0617584;AF=0.000139076 GT:DR:DV 0/0:251626:35 +chr20 4686077 21 CCTCATTCCTGAG N . STRANDBIAS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4686088;STD_quant_start=3.444234;STD_quant_stop=5.277589;Kurtosis_quant_start=-1.396320;Kurtosis_quant_stop=-1.716715;SVTYPE=DEL;SUPTYPE=AL;SVLEN=-11;STRANDS=+-;STRANDS2=148,57,148,57;RE=205;REF_strand=130557,120967;Strandbias_pval=4.04751e-09;AF=0.000815032 GT:DR:DV 0/0:251319:205 +chr20 4686090 22 TTTCTCGATTTCTCCATTATGTAACGGGGAGC N . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4686123;STD_quant_start=8.031189;STD_quant_stop=3.286335;Kurtosis_quant_start=-1.697654;Kurtosis_quant_stop=-0.788409;SVTYPE=DEL;SUPTYPE=AL;SVLEN=-33;STRANDS=+-;STRANDS2=9,11,9,11;RE=20;REF_strand=130434,121022;Strandbias_pval=0.656011;AF=7.95368e-05 GT:DR:DV 0/0:251436:20 +chr20 4686108 23 N TACTACCTGCTCT . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4686110;STD_quant_start=7.071068;STD_quant_stop=5.205766;Kurtosis_quant_start=-2.067216;Kurtosis_quant_stop=-1.912930;SVTYPE=INS;SUPTYPE=AL;SVLEN=11;STRANDS=+-;STRANDS2=15,4,15,4;RE=19;REF_strand=130421,121035;Strandbias_pval=0.0207633;AF=7.55599e-05 GT:DR:DV 0/0:251437:19 +chr20 4686162 24 N CTTTTTTTTTTT . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4686163;STD_quant_start=0.000000;STD_quant_stop=2.859453;Kurtosis_quant_start=-0.858622;Kurtosis_quant_stop=-1.664473;SVTYPE=INS;SUPTYPE=AL;SVLEN=11;STRANDS=+-;STRANDS2=26,9,26,9;RE=35;REF_strand=130129,121162;Strandbias_pval=0.010149;AF=0.000139281 GT:DR:DV 0/0:251256:35 +chr20 4686210 25 GCAGGCGGTATCAACTGATGCAAGTGTTCAA N . STRANDBIAS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4686234;STD_quant_start=7.976354;STD_quant_stop=7.061633;Kurtosis_quant_start=-1.824385;Kurtosis_quant_stop=-1.074888;SVTYPE=DEL;SUPTYPE=AL,NR;SVLEN=-24;STRANDS=+-;STRANDS2=73,18,73,18;RE=91;REF_strand=129814,121315;Strandbias_pval=2.15973e-08;AF=0.000362364 GT:DR:DV 0/0:251038:91 +chr20 4686249 26 N TTTTTTTTTTTTT . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4686249;STD_quant_start=2.804758;STD_quant_stop=4.434712;Kurtosis_quant_start=-1.419676;Kurtosis_quant_stop=-1.435046;SVTYPE=INS;SUPTYPE=AL;SVLEN=13;STRANDS=+-;STRANDS2=23,8,23,8;RE=31;REF_strand=129612,121376;Strandbias_pval=0.0119593;AF=0.000123512 GT:DR:DV 0/0:250957:31 +chr20 4686326 27 GGGGGCACAGAGTGTGCGCCGGGCCGCGCGGCAATTGGTCCCCGCGCCGACCTCCGCCCGCGAGCGCCGCCGCTTCCCTTCCCCGCCCCGCGTCCCTCCCCCTCGGCCCCGCGCGTCGCCTGTCCTCCGAGCCAGTCGCTGACAGCCGCGGCGCCGCGAGCTTCTCCTCTCCTCACGACCGAGGCAGGTAAACGCCCGGGGTGGGAGGAACGCGGGCGGGGGCAGGGGAGCCGCGGGGGCCGAGTGAGGACCCCGGGCCTCGGGTCCCAGGCGCAAGGGTGCCCGGCCGGGCGGGGTCGGGACCCCAGTGAGGAGGGGCCGGGGGCTGCCCCGCGGGCGCGTGACGCGTCTCGGGCCTGCCCGGCTGCGCTGGTCTCCGCTCGGGTGAGGCGGCTTGGCTTCGCTTTTCAGGTTAGGAAAGCTCCCTTTACTGCGCGTTGGGGGGCTGGGGGAGCTGGCGGAGCCCCGTTAGGGAGGTCGGTGGCGCCGGGGTGTCTCAGCGCCCCCTGCACCCCGCGCGGGTCCGGCCCAGCGGGCGATCGCTGGCGCCCAGGGAACTCCGGGAGGGCCGCCAGCGGGCTCCGCAGGGCGCGGGGCGGGGAGGGGCGCCTGGGGGCCGCGGGGCTCGCGCTCCCCGCCCGTTGGCCGCCCCTCGGAGGCCGAGATCGGGGCCCAGAACGCCCCTTGGCAAGGCCTGGCGCTTCCGCGATGCCCAGAGGGTGCTTGGGGGGATGGAGAGAGGGGCGCCCGCCG N . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4687079;STD_quant_start=0.000000;STD_quant_stop=0.000000;Kurtosis_quant_start=-0.139152;Kurtosis_quant_stop=2.586990;SVTYPE=DEL;SUPTYPE=AL;SVLEN=-753;STRANDS=+-;STRANDS2=43,48,43,48;RE=91;REF_strand=127320,122858;Strandbias_pval=0.529759;AF=0.000363741 GT:DR:DV 0/0:250087:91 +chr20 4686326 28 N GCCGCGCAGCG . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4686329;STD_quant_start=8.043631;STD_quant_stop=8.062258;Kurtosis_quant_start=-1.946353;Kurtosis_quant_stop=-1.895225;SVTYPE=INS;SUPTYPE=AL;SVLEN=11;STRANDS=+-;STRANDS2=9,9,9,9;RE=18;REF_strand=128962,121573;Strandbias_pval=1;AF=7.18462e-05 GT:DR:DV 0/0:250517:18 +chr20 4686335 29 GAGTGTGCGCCGGGCCGCGCGGCAATTGGTCCCCGCGCCGACCTCCGCCCGCGAGCGCCGCCGCTTCCCTTCCCCGCCCCGCG N . PASS IMPRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4686394;STD_quant_start=13.722245;STD_quant_stop=12.541930;Kurtosis_quant_start=1.276270;Kurtosis_quant_stop=-0.724537;SVTYPE=DEL;SUPTYPE=AL;SVLEN=-59;STRANDS=+-;STRANDS2=4,7,4,7;RE=11;REF_strand=128746,121667;Strandbias_pval=0.375994;AF=4.39274e-05 GT:DR:DV 0/0:250402:11 +chr20 4686444 30 GCGTCGCCTGTCCTCCGAGCCAGTCGCTGACAGCCGCGGCGCCGCGAGCTTCTCCTCTCCTCACGACCGAGGCAGGTAAACGCCCGGGGTGGGAGGAACGCGGG N . PASS IMPRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4686542;STD_quant_start=16.272676;STD_quant_stop=12.853015;Kurtosis_quant_start=-1.926000;Kurtosis_quant_stop=-1.760143;SVTYPE=DEL;SUPTYPE=AL;SVLEN=-98;STRANDS=+-;STRANDS2=10,7,10,7;RE=17;REF_strand=127983,122013;Strandbias_pval=0.630738;AF=6.80011e-05 GT:DR:DV 0/0:249979:17 +chr20 4686423 31 N CCCCCCCCCCCCCCCC . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4686431;STD_quant_start=5.063236;STD_quant_stop=5.300086;Kurtosis_quant_start=-1.379149;Kurtosis_quant_stop=-1.502763;SVTYPE=INS;SUPTYPE=AL;SVLEN=11;STRANDS=+-;STRANDS2=6,17,6,17;RE=23;REF_strand=128339,121824;Strandbias_pval=0.020175;AF=9.19401e-05 GT:DR:DV 0/0:250140:23 +chr20 4686486 32 CTTCTCCTCTC N . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4686497;STD_quant_start=2.442083;STD_quant_stop=2.814301;Kurtosis_quant_start=-0.668017;Kurtosis_quant_stop=-0.752107;SVTYPE=DEL;SUPTYPE=AL;SVLEN=-11;STRANDS=+-;STRANDS2=148,128,148,128;RE=276;REF_strand=127994,121991;Strandbias_pval=0.433948;AF=0.00110407 GT:DR:DV 0/0:249709:276 +chr20 4686538 33 CGGGCGGGGGCAGGGGAGCCGCGGGGGCCGAGTGAGGACCCCGGGCCTCGGGTCCCAGGCGCAAGGGTGCCCGGCCGGGCGGGGTCGGGACCCCAGTGAGGAGGGGCCGGGGGCTGCCCCGCGGGCGCGTGACGCGTCTCGGGCCTGCCCGGCTGCGCTGGTCTCCGCTCGGGTGAGGCGGCTTGGCTTCGCTTTTCAGGTTAGGAAAGCTCCCTTTACTGCGCGTTGGGGGGCTGGGGGAGCTGGCGGAGCCCCGTTAGGGAGGTCGGTGGCGCCGGGGTGTCTCAGCGCCCCCTGCACCCCGCGCGGGTCCGGCCCAGCGGGCGATCGCTGGCGCCCAGGGAACTCCGGGAGGGCCGCCAGCGGGCTCCGCAGGGCGCGGGGCGGGGAGGGGCGCCTGGGGGCCGCGGGGCTCGCGCTCCCCGCCCGTTGGCCGCCCCTCGGAGGCCGAGATCGGGGCCCAGAACGCCCCTTGGCAAGGCCTGGCGCTTCCGCGATGCCCAGAGGGTGCTTGGGGGGATGGAGAGAGGGGCGCCCGCCGGGGGAGTTCCGGGAGCCTCGGTGCCTCCCGCCGCAGCTGCAGCGTTCCTCCCGGGAGGCGGCCCAGCCCTTCATCCTCGCCGCCTGAGCTTCTCCGAGGGGGGCTGCAGCCTTGCGGCCGTTGCCACCGCCTGGAGAAGCGGCCCACGCGGACTGA N . STRANDBIAS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4687235;STD_quant_start=3.130495;STD_quant_stop=3.478505;Kurtosis_quant_start=-1.228558;Kurtosis_quant_stop=-0.916254;SVTYPE=DEL;SUPTYPE=AL;SVLEN=-697;STRANDS=+-;STRANDS2=16,3,16,3;RE=19;REF_strand=126410,123255;Strandbias_pval=0.00448082;AF=7.6102e-05 GT:DR:DV 0/0:249646:19 +chr20 4686532 34 AACGCGGGCGGGGGCAGGGGAGCCGCGGGGGCCGAGTGAGGACCCCGGGCCTCGGGTCCCAGGCGCAAGGGTGCCCGGCCGGGCGGGGTCGGGACCCCAGTGAGGAGGGGCCGGGGGCTGCCCCGCGGGCGCGTGACGCGTCTCGGGCCTGC N . PASS IMPRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4686685;STD_quant_start=20.883007;STD_quant_stop=23.121419;Kurtosis_quant_start=-0.604897;Kurtosis_quant_stop=-0.758432;SVTYPE=DEL;SUPTYPE=AL,NR;SVLEN=-153;STRANDS=+-;STRANDS2=9,2,9,2;RE=11;REF_strand=127483,122410;Strandbias_pval=0.0660233;AF=4.40188e-05 GT:DR:DV 0/0:249882:11 +chr20 4686529 35 N AAGGCGAAGGAAGGAAGGGGACGGAAGGA . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4686544;STD_quant_start=8.258329;STD_quant_stop=5.385165;Kurtosis_quant_start=-2.103326;Kurtosis_quant_stop=-1.723307;SVTYPE=INS;SUPTYPE=AL;SVLEN=11;STRANDS=+-;STRANDS2=13,6,13,6;RE=19;REF_strand=127734,122128;Strandbias_pval=0.169088;AF=7.6042e-05 GT:DR:DV 0/0:249843:19 +chr20 4686576 36 CGCGGGGGCCGAGTGAGGACCCCGGGCCTCGGGTCCCA N . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4686595;STD_quant_start=4.441374;STD_quant_stop=4.484741;Kurtosis_quant_start=-0.161669;Kurtosis_quant_stop=-0.759767;SVTYPE=DEL;SUPTYPE=AL;SVLEN=-19;STRANDS=+-;STRANDS2=53,72,53,72;RE=125;REF_strand=127550,122351;Strandbias_pval=0.0599634;AF=0.000500198 GT:DR:DV 0/0:249776:125 +chr20 4686538 37 CGGGCGGGGGCAGGGGAGCCGCGGGGGCCGAGTGAGGACCCCGGGCCTCGGGTCCCAGGCGCAAGGGTGCCCGGCCGGGCGGGGTCGGGACCCCAGTGAGGAGGGGCCGGGGGCTGCCCCGCGGGCGCGTGACGCGTCTCGGGCCTGCCCGGCTGCGCTGGTCTCCGCTCGGGTGAGGCGGCTTGGCTTCGCTTTTCAGGTTAGGAAAGCTCCCTTTACTGCGCGTTGGGGGGCTGGGGGAGCTGGCGGAGCCCCGTTAGGGAGGTCGGTGGCGCCGGGGTGTCTCAGCGCCCCCTGCACCCCGCGCGGGTCCGGCCCAGCGGGCGATCGCTGGCGCCCAGGGAACTCCGGGAGGGCCGCCAGCGGGCTCCGCAGGGCGCGGGGCGGGGAGGGGCGCCTGGGGGCCGCGGGGCTCGCGCTCCCCGCCCGTTGGCCGCCCCTCGGAGGCCGAGATCGGGGCCCAGAACGCCCCTTGGCAAGGCCTGGCGCTTCCGCGATGCCCAGAGGGTGCTTGGGGGGATGGAGAGAGGGGCGCCCGCCGGGGGAGTTCCGGGAGCCTCGGTGCCTCCCGCCGCAGCTGCAGCGTTCCTCCCGGGAGGCGGCCCAGCCCTTCATCCTCGCCGCCTGAGCTTCTCCGAGGGGGGCTGCAGCCTTGCGGCCGTTGCCACCGCCTGGAGAAGCGGCCCACGCGGACTGA N . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4687235;STD_quant_start=1.581139;STD_quant_stop=2.213594;Kurtosis_quant_start=3.501267;Kurtosis_quant_stop=-1.056534;SVTYPE=DEL;SUPTYPE=AL;SVLEN=-697;STRANDS=+-;STRANDS2=27,33,27,33;RE=60;REF_strand=126410,123255;Strandbias_pval=0.438962;AF=0.000240322 GT:DR:DV 0/0:249605:60 +chr20 4686579 38 N GGGGGCGGGCGCGGGCGG . PASS IMPRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4686589;STD_quant_start=9.208692;STD_quant_stop=11.653326;Kurtosis_quant_start=-1.461144;Kurtosis_quant_stop=-1.306908;SVTYPE=INS;SUPTYPE=AL;SVLEN=16;STRANDS=+-;STRANDS2=6,5,6,5;RE=11;REF_strand=127558,122342;Strandbias_pval=1;AF=4.40176e-05 GT:DR:DV 0/0:249889:11 +chr20 4686637 39 GGAGGGGCCGGGGG N . STRANDBIAS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4686653;STD_quant_start=7.412624;STD_quant_stop=8.110326;Kurtosis_quant_start=-1.717684;Kurtosis_quant_stop=-1.859802;SVTYPE=DEL;SUPTYPE=AL,NR;SVLEN=-16;STRANDS=+-;STRANDS2=245,321,245,321;RE=566;REF_strand=127359,122581;Strandbias_pval=0.000288483;AF=0.00226454 GT:DR:DV 0/0:249374:566 +chr20 4686675 40 CTCGGGCCTGCCCGGCTGCGCTGGTCTC N . STRANDBIAS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4686700;STD_quant_start=1.927248;STD_quant_stop=9.662150;Kurtosis_quant_start=-1.248368;Kurtosis_quant_stop=-1.491278;SVTYPE=DEL;SUPTYPE=AL;SVLEN=-25;STRANDS=+-;STRANDS2=22,6,22,6;RE=28;REF_strand=127212,122727;Strandbias_pval=0.00386803;AF=0.000112027 GT:DR:DV 0/0:249911:28 +chr20 4686673 41 TTGGCTTCGCT N . PASS IMPRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4686731;STD_quant_start=14.235578;STD_quant_stop=8.731320;Kurtosis_quant_start=-1.984032;Kurtosis_quant_stop=-1.802030;SVTYPE=DEL;SUPTYPE=AL;SVLEN=-58;STRANDS=+-;STRANDS2=81,97,81,97;RE=178;REF_strand=127128,122776;Strandbias_pval=0.154964;AF=0.000712274 GT:DR:DV 0/0:249726:178 +chr20 4686768 42 GGGCTGGGGGA N . STRANDBIAS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4686779;STD_quant_start=5.841935;STD_quant_stop=5.794191;Kurtosis_quant_start=-0.361337;Kurtosis_quant_stop=-0.608824;SVTYPE=DEL;SUPTYPE=AL,NR;SVLEN=-11;STRANDS=+-;STRANDS2=83,151,83,151;RE=234;REF_strand=126793,123022;Strandbias_pval=2.93761e-06;AF=0.000936693 GT:DR:DV 0/0:249581:234 +chr20 4686805 43 GGTGGCGCCGG N . STRANDBIAS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4686816;STD_quant_start=4.100618;STD_quant_stop=5.387708;Kurtosis_quant_start=-1.621477;Kurtosis_quant_stop=-0.897819;SVTYPE=DEL;SUPTYPE=AL;SVLEN=-11;STRANDS=+-;STRANDS2=116,177,116,177;RE=293;REF_strand=126652,123164;Strandbias_pval=0.000172996;AF=0.00117286 GT:DR:DV 0/0:249523:293 +chr20 4686815 44 GGGGTGTCTCAGCGCCCCCTGCACCCCGCGCGGGTCCGGCCCAGCGGGCGATCGCTGGCGCCCAGGGAACTCCGGGAGGGCCGCCAGCGGGCTCCGCAGGGCGCGGGGCGGGGAGGGGCGCCT N . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4686937;STD_quant_start=5.924525;STD_quant_stop=5.822371;Kurtosis_quant_start=0.208164;Kurtosis_quant_stop=-0.417349;SVTYPE=DEL;SUPTYPE=AL;SVLEN=-122;STRANDS=+-;STRANDS2=5,8,5,8;RE=13;REF_strand=126395,123370;Strandbias_pval=0.418654;AF=5.20489e-05 GT:DR:DV 0/0:249752:13 +chr20 4686928 45 GGGCGCCTGGGGGCC N . STRANDBIAS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4686944;STD_quant_start=1.665986;STD_quant_stop=1.511858;Kurtosis_quant_start=2.670211;Kurtosis_quant_stop=3.201811;SVTYPE=DEL;SUPTYPE=AL;SVLEN=-16;STRANDS=+-;STRANDS2=59,138,59,138;RE=197;REF_strand=126168,123565;Strandbias_pval=7.34039e-09;AF=0.000788842 GT:DR:DV 0/0:249536:197 +chr20 4686947 46 CCGCCCGTTGG N . STRANDBIAS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4686971;STD_quant_start=6.333208;STD_quant_stop=9.053544;Kurtosis_quant_start=-1.516175;Kurtosis_quant_stop=-1.424300;SVTYPE=DEL;SUPTYPE=AL,NR;SVLEN=-24;STRANDS=+-;STRANDS2=250,171,250,171;RE=421;REF_strand=126091,123665;Strandbias_pval=0.000296568;AF=0.00168565 GT:DR:DV 0/0:249335:421 +chr20 4686984 47 N CGCCTCCTCCTCCTTCCGTCGTCTCT . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4686995;STD_quant_start=7.757694;STD_quant_stop=6.223124;Kurtosis_quant_start=-1.414040;Kurtosis_quant_stop=-1.935750;SVTYPE=INS;SUPTYPE=AL;SVLEN=12;STRANDS=+-;STRANDS2=10,12,10,12;RE=22;REF_strand=125970,123786;Strandbias_pval=0.675182;AF=8.8086e-05 GT:DR:DV 0/0:249734:22 +chr20 4687005 48 CCCTTGGCAAG N . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4687018;STD_quant_start=4.047221;STD_quant_stop=4.884670;Kurtosis_quant_start=-1.203357;Kurtosis_quant_stop=-0.029027;SVTYPE=DEL;SUPTYPE=AL;SVLEN=-13;STRANDS=+-;STRANDS2=58,42,58,42;RE=100;REF_strand=125883,123897;Strandbias_pval=0.134378;AF=0.000400352 GT:DR:DV 0/0:249680:100 +chr20 4687060 49 TGGAGAGAGGGGCGCCCGCCGGGGGAGTTCCGGGAGCCTCGGTGCCTCCCGCCGCAGCTGCAGCGTTCCTCCCGGGAGGCGGCCCAGCCCTTCATCCTCGCCGCCTGAG N . PASS IMPRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4687159;STD_quant_start=14.963288;STD_quant_stop=15.076472;Kurtosis_quant_start=2.339562;Kurtosis_quant_stop=-1.026487;SVTYPE=DEL;SUPTYPE=AL,NR;SVLEN=-99;STRANDS=+-;STRANDS2=6,4,6,4;RE=10;REF_strand=125556,124224;Strandbias_pval=0.753936;AF=4.00352e-05 GT:DR:DV 0/0:249770:10 +chr20 4687066 50 GGGGCGCCCGCCGG N . STRANDBIAS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4687087;STD_quant_start=8.849462;STD_quant_stop=8.714514;Kurtosis_quant_start=-1.777666;Kurtosis_quant_stop=-1.824511;SVTYPE=DEL;SUPTYPE=AL,NR;SVLEN=-21;STRANDS=+-;STRANDS2=203,321,203,321;RE=524;REF_strand=125682,124153;Strandbias_pval=1.36243e-07;AF=0.00209738 GT:DR:DV 0/0:249311:524 +chr20 4687049 51 N GGGGGGGGGGGGGGGG . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4687054;STD_quant_start=3.162278;STD_quant_stop=4.669047;Kurtosis_quant_start=-0.674649;Kurtosis_quant_stop=-0.494919;SVTYPE=INS;SUPTYPE=AL;SVLEN=11;STRANDS=+-;STRANDS2=13,5,13,5;RE=18;REF_strand=125748,124039;Strandbias_pval=0.096381;AF=7.20614e-05 GT:DR:DV 0/0:249769:18 +chr20 4687120 52 GCGTTCCTCCCGGGAGGCGGCCCAGCC N . STRANDBIAS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4687137;STD_quant_start=4.068852;STD_quant_stop=4.325634;Kurtosis_quant_start=-1.460869;Kurtosis_quant_stop=-0.865142;SVTYPE=DEL;SUPTYPE=AL;SVLEN=-17;STRANDS=+-;STRANDS2=69,22,69,22;RE=91;REF_strand=125487,124311;Strandbias_pval=8.36705e-07;AF=0.000364294 GT:DR:DV 0/0:249707:91 +chr20 4687099 53 N GCCAACCTGCTGG . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4687106;STD_quant_start=9.186947;STD_quant_stop=8.012490;Kurtosis_quant_start=-0.672295;Kurtosis_quant_stop=0.204541;SVTYPE=INS;SUPTYPE=AL;SVLEN=11;STRANDS=+-;STRANDS2=8,4,8,4;RE=12;REF_strand=125599,124239;Strandbias_pval=0.38777;AF=4.80311e-05 GT:DR:DV 0/0:249826:12 +chr20 4687163 54 N TGGCATGGAAG . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4687166;STD_quant_start=6.589132;STD_quant_stop=6.000000;Kurtosis_quant_start=-1.965332;Kurtosis_quant_stop=-1.753338;SVTYPE=INS;SUPTYPE=AL;SVLEN=11;STRANDS=+-;STRANDS2=11,14,11,14;RE=25;REF_strand=125377,124370;Strandbias_pval=0.555653;AF=0.000100101 GT:DR:DV 0/0:249722:25 +chr20 4687254 55 CCTCGGGCCTCGGCGGGGGCGGGGTC N . PASS IMPRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4687276;STD_quant_start=8.629736;STD_quant_stop=11.320853;Kurtosis_quant_start=-1.372174;Kurtosis_quant_stop=-1.679964;SVTYPE=DEL;SUPTYPE=AL;SVLEN=-22;STRANDS=+-;STRANDS2=248,222,248,222;RE=470;REF_strand=124959,124368;Strandbias_pval=0.26782;AF=0.00188507 GT:DR:DV 0/0:248857:470 +chr20 4687217 56 CTGGAGAAGCGGCCCACGCGGACTGACGGGCGGGGGCGGGGCCTCGGGCCTCGGCGGGGGCGGGGTCCGGGGAGGCCCCACCCTCTGTTCTCCAGGGGCGGGGAGAGAGGAGCTGCA N . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4687326;STD_quant_start=9.165151;STD_quant_stop=7.563068;Kurtosis_quant_start=-1.310573;Kurtosis_quant_stop=-0.745943;SVTYPE=DEL;SUPTYPE=AL;SVLEN=-109;STRANDS=+-;STRANDS2=6,9,6,9;RE=15;REF_strand=124968,124369;Strandbias_pval=0.453408;AF=6.01595e-05 GT:DR:DV 0/0:249322:15 +chr20 4687212 57 N CTGTGCCCGCCCCGTCGCCGCCCTCGATCTGCGATGCCCACC . PASS IMPRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4687237;STD_quant_start=12.934450;STD_quant_stop=9.402127;Kurtosis_quant_start=-1.795650;Kurtosis_quant_stop=-1.517337;SVTYPE=INS;SUPTYPE=AL;SVLEN=12;STRANDS=+-;STRANDS2=11,5,11,5;RE=16;REF_strand=125161,124370;Strandbias_pval=0.210136;AF=6.41203e-05 GT:DR:DV 0/0:249515:16 +chr20 4687290 58 CCTCTGTTCTCCAGGGGCGGGGAGAGAGGAGCTGCAGGTCTGCGGCCTGGCCCCAGGTGCGATGGCGGACCCCAGCTTGGCCAGTCACATT N . PASS IMPRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4687396;STD_quant_start=22.986953;STD_quant_stop=28.979303;Kurtosis_quant_start=-0.411859;Kurtosis_quant_stop=1.226977;SVTYPE=DEL;SUPTYPE=AL;SVLEN=-106;STRANDS=+-;STRANDS2=5,5,5,5;RE=10;REF_strand=124686,124367;Strandbias_pval=1;AF=4.01521e-05 GT:DR:DV 0/0:249043:10 +chr20 4687292 59 N TGCTCCCCCTC . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4687298;STD_quant_start=5.484828;STD_quant_stop=4.760952;Kurtosis_quant_start=-1.188103;Kurtosis_quant_stop=-1.362116;SVTYPE=INS;SUPTYPE=AL;SVLEN=12;STRANDS=+-;STRANDS2=13,11,13,11;RE=24;REF_strand=124823,124368;Strandbias_pval=0.838818;AF=9.63117e-05 GT:DR:DV 0/0:249167:24 +chr20 4687508 60 ATGGGGAGAAATCC N . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4687527;STD_quant_start=3.067424;STD_quant_stop=2.820380;Kurtosis_quant_start=-2.205808;Kurtosis_quant_stop=-1.503002;SVTYPE=DEL;SUPTYPE=AL;SVLEN=-19;STRANDS=+-;STRANDS2=28,16,28,16;RE=44;REF_strand=124189,124364;Strandbias_pval=0.0722459;AF=0.000177025 GT:DR:DV 0/0:248509:44 +chr20 4687540 61 TTTGCTCTTCTC N . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4687566;STD_quant_start=7.065376;STD_quant_stop=9.261216;Kurtosis_quant_start=-1.672284;Kurtosis_quant_stop=-1.906482;SVTYPE=DEL;SUPTYPE=AL,NR;SVLEN=-26;STRANDS=+-;STRANDS2=87,88,87,88;RE=175;REF_strand=124061,124362;Strandbias_pval=1;AF=0.000704444 GT:DR:DV 0/0:248248:175 +chr20 4687590 62 N TTTTTTTTTTTTTTTTTTT . STRANDBIAS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4687590;STD_quant_start=0.000000;STD_quant_stop=2.347576;Kurtosis_quant_start=-0.751408;Kurtosis_quant_stop=-0.466328;SVTYPE=INS;SUPTYPE=AL;SVLEN=11;STRANDS=+-;STRANDS2=75,15,75,15;RE=90;REF_strand=123926,124362;Strandbias_pval=5.12582e-11;AF=0.000362482 GT:DR:DV 0/0:248198:90 +chr20 4687590 63 N TTTTTTTTTTTTTTTTTTTTTTTTTTTTTT . STRANDBIAS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4687593;STD_quant_start=4.472136;STD_quant_stop=2.121320;Kurtosis_quant_start=1.650206;Kurtosis_quant_stop=4.485074;SVTYPE=INS;SUPTYPE=AL;SVLEN=22;STRANDS=+-;STRANDS2=11,1,11,1;RE=12;REF_strand=123922,124362;Strandbias_pval=0.00336707;AF=4.83317e-05 GT:DR:DV 0/0:248272:12 +chr20 4687584 64 TTTTTTTAACCTC N . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4687606;STD_quant_start=6.067270;STD_quant_stop=6.640340;Kurtosis_quant_start=-1.022668;Kurtosis_quant_stop=-0.770309;SVTYPE=DEL;SUPTYPE=AL;SVLEN=-22;STRANDS=+-;STRANDS2=84,87,84,87;RE=171;REF_strand=123926,124362;Strandbias_pval=0.878491;AF=0.000688716 GT:DR:DV 0/0:248117:171 +chr20 4687660 65 N TTTTTTTTTTTTTTTTTTTTTTTTT . STRANDBIAS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4687660;STD_quant_start=3.118858;STD_quant_stop=8.039674;Kurtosis_quant_start=-1.678181;Kurtosis_quant_stop=-1.882811;SVTYPE=INS;SUPTYPE=AL;SVLEN=27;STRANDS=+-;STRANDS2=19,4,19,4;RE=23;REF_strand=123738,124362;Strandbias_pval=0.00150537;AF=9.27046e-05 GT:DR:DV 0/0:248077:23 +chr20 4687635 66 GCCATCGCAGAGCCACA N . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4687663;STD_quant_start=7.158604;STD_quant_stop=4.565315;Kurtosis_quant_start=-2.046208;Kurtosis_quant_stop=-0.357305;SVTYPE=DEL;SUPTYPE=AL,NR;SVLEN=-28;STRANDS=+-;STRANDS2=55,60,55,60;RE=115;REF_strand=123772,124362;Strandbias_pval=0.70935;AF=0.000463459 GT:DR:DV 0/0:248019:115 +chr20 4687783 67 CCCATATGATT N . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4687797;STD_quant_start=5.156913;STD_quant_stop=5.341465;Kurtosis_quant_start=-1.606711;Kurtosis_quant_stop=-1.906903;SVTYPE=DEL;SUPTYPE=AL;SVLEN=-14;STRANDS=+-;STRANDS2=58,70,58,70;RE=128;REF_strand=123326,124348;Strandbias_pval=0.33135;AF=0.000516808 GT:DR:DV 0/0:247546:128 +chr20 4687810 68 TTTCCTTAGGGAAAACTCCTGGTAGAATA N . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4687828;STD_quant_start=4.690416;STD_quant_stop=1.381699;Kurtosis_quant_start=-0.934609;Kurtosis_quant_stop=-0.646630;SVTYPE=DEL;SUPTYPE=AL;SVLEN=-18;STRANDS=+-;STRANDS2=7,15,7,15;RE=22;REF_strand=123229,124341;Strandbias_pval=0.133871;AF=8.88638e-05 GT:DR:DV 0/0:247548:22 +chr20 4687912 69 N . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4687932;STD_quant_start=2.645751;STD_quant_stop=4.289522;Kurtosis_quant_start=0.975077;Kurtosis_quant_stop=-0.453591;SVTYPE=DEL;SUPTYPE=AL,NR;SVLEN=-20;STRANDS=+-;STRANDS2=10,7,10,7;RE=17;REF_strand=122851,124325;Strandbias_pval=0.478146;AF=6.87769e-05 GT:DR:DV 0/0:247159:17 +chr20 4687912 70 N AAAAAAAAAAAAAAAAAAAAA . STRANDBIAS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4687920;STD_quant_start=0.462910;STD_quant_stop=6.071008;Kurtosis_quant_start=-0.252578;Kurtosis_quant_stop=-1.130183;SVTYPE=INS;SUPTYPE=AL;SVLEN=13;STRANDS=+-;STRANDS2=5,23,5,23;RE=28;REF_strand=122865,124326;Strandbias_pval=0.00091678;AF=0.000113273 GT:DR:DV 0/0:247163:28 +chr20 4687941 71 TCAACAACGCTCTT N . PASS IMPRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4687972;STD_quant_start=12.219873;STD_quant_stop=10.527074;Kurtosis_quant_start=-1.785346;Kurtosis_quant_stop=-1.886198;SVTYPE=DEL;SUPTYPE=AL;SVLEN=-31;STRANDS=+-;STRANDS2=90,77,90,77;RE=167;REF_strand=122667,124295;Strandbias_pval=0.279616;AF=0.000676217 GT:DR:DV 0/0:246795:167 +chr20 4687949 72 N AAAAAAAAAAAAAAAAAAAAAAAAA . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4687952;STD_quant_start=0.674200;STD_quant_stop=3.045115;Kurtosis_quant_start=-1.260984;Kurtosis_quant_stop=-1.707417;SVTYPE=INS;SUPTYPE=AL;SVLEN=11;STRANDS=+-;STRANDS2=5,18,5,18;RE=23;REF_strand=122716,124299;Strandbias_pval=0.0106547;AF=9.31118e-05 GT:DR:DV 0/0:246992:23 +chr20 4688011 73 N AAAAAAAAAAAAA . STRANDBIAS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4688014;STD_quant_start=0.000000;STD_quant_stop=1.669046;Kurtosis_quant_start=-0.305271;Kurtosis_quant_stop=-1.239728;SVTYPE=INS;SUPTYPE=AL;SVLEN=11;STRANDS=+-;STRANDS2=7,22,7,22;RE=29;REF_strand=122038,124029;Strandbias_pval=0.00818594;AF=0.000117854 GT:DR:DV 0/0:246038:29 +chr20 28640926 74 N TTTCTTTCTTTCTTTCTTTCTTTCTTTCT . PASS IMPRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=28640927;STD_quant_start=11.171392;STD_quant_stop=11.406139;Kurtosis_quant_start=-1.762587;Kurtosis_quant_stop=-1.259846;SVTYPE=INS;SUPTYPE=AL;SVLEN=28;STRANDS=+-;STRANDS2=6,9,6,9;RE=15;REF_strand=40,62;Strandbias_pval=1;AF=0.147059 GT:DR:DV 0/0:87:15 +chr20 28640960 75 N TTTCTTTCTTTCTTTCTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCCTTTCTTTCTTTCTTTCTTTCTTTCTCTTTCTTTCCTTCCTTCCTTCTTTCCTCT . PASS IMPRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=28640960;STD_quant_start=14.058320;STD_quant_stop=4.700097;Kurtosis_quant_start=-2.117696;Kurtosis_quant_stop=-1.833176;SVTYPE=INS;SUPTYPE=AL;SVLEN=117;STRANDS=+-;STRANDS2=9,13,9,13;RE=22;REF_strand=40,62;Strandbias_pval=1;AF=0.215686 GT:DR:DV 0/0:80:22 +chr20 28641010 76 N CTTTCATTTATTTTCCTTTCCTTTCCTTT . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=28641010;STD_quant_start=1.040833;STD_quant_stop=2.516611;Kurtosis_quant_start=-0.405494;Kurtosis_quant_stop=-1.560766;SVTYPE=INS;SUPTYPE=AL;SVLEN=29;STRANDS=+-;STRANDS2=11,13,11,13;RE=24;REF_strand=40,62;Strandbias_pval=0.645417;AF=0.235294 GT:DR:DV 0/0:78:24 +chr20 28641148 77 N CTTCTTCCTTCCTTCCTTCCT . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=28641148;STD_quant_start=2.387467;STD_quant_stop=3.464102;Kurtosis_quant_start=-0.296724;Kurtosis_quant_stop=2.502504;SVTYPE=INS;SUPTYPE=AL;SVLEN=26;STRANDS=+-;STRANDS2=6,7,6,7;RE=13;REF_strand=40,62;Strandbias_pval=0.765411;AF=0.127451 GT:DR:DV 0/0:89:13 diff --git a/SVs_sniffles/vcf/55492_bodySnif.vcf b/SVs_sniffles/vcf/55492_bodySnif.vcf new file mode 100644 index 0000000..02deba4 --- /dev/null +++ b/SVs_sniffles/vcf/55492_bodySnif.vcf @@ -0,0 +1,39 @@ +##fileformat=VCFv4.1 +##source=Sniffles +##fileDate=20210810:56:43 AMef_minus +##contig= +##ALT= +##ALT= +##ALT= +##ALT= +##ALT= +##ALT= +##FILTER= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##FORMAT= +##FORMAT= +##FORMAT= +#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT bamfilt/55492_f.bam +chr20 4699380 0 N GGTGGTGCTGGGGGCAGCTCCTCATGGTGGTGGCTGGGGCAGCCCTCATGGTGGTGCTGGGGGCAGCCTCATGGTGGTGGCTGGGGGCAGCTCAT . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4699380;STD_quant_start=0.000000;STD_quant_stop=1.212150;Kurtosis_quant_start=47.606152;Kurtosis_quant_stop=0.885804;SVTYPE=INS;SUPTYPE=AL;SVLEN=95;STRANDS=+-;STRANDS2=527,483,527,483;RE=1010;REF_strand=6586,6988;Strandbias_pval=0.0264808;AF=0.074407 GT:DR:DV 0/0:12564:1010 +chr20 4699439 1 N GGGGCAGCCTCATGGTGGTGGCTAGTGGGGCAGCCTCATGGTGGTGGCTGGGGGGCAGCCTCATGGTGGTGGCT . PASS IMPRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4699439;STD_quant_start=9.853908;STD_quant_stop=10.140456;Kurtosis_quant_start=-1.876406;Kurtosis_quant_stop=131.667373;SVTYPE=INS;SUPTYPE=AL;SVLEN=94;STRANDS=+-;STRANDS2=982,1028,982,1028;RE=2010;REF_strand=6584,6988;Strandbias_pval=0.774238;AF=0.148099 GT:DR:DV 0/0:11562:2010 +chr20 4699391 2 N GGGCAGCCTCATGATGGTGGCTGGGGGCAGCCTCATGGTGGTGGGCTAGCAGCTCATGGTGGTGGCTGGGGGCAGCCTCATGGTGGTGGCT . STRANDBIAS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4699391;STD_quant_start=0.738831;STD_quant_stop=3.772790;Kurtosis_quant_start=-1.032456;Kurtosis_quant_stop=-1.118477;SVTYPE=INS;SUPTYPE=AL;SVLEN=92;STRANDS=+-;STRANDS2=148,289,148,289;RE=437;REF_strand=6586,6988;Strandbias_pval=1.29225e-09;AF=0.0321939 GT:DR:DV 0/0:13137:437 diff --git a/SVs_sniffles/vcf/55492_promoterSnif.vcf b/SVs_sniffles/vcf/55492_promoterSnif.vcf new file mode 100644 index 0000000..10a9d63 --- /dev/null +++ b/SVs_sniffles/vcf/55492_promoterSnif.vcf @@ -0,0 +1,37 @@ +##fileformat=VCFv4.1 +##source=Sniffles +##fileDate=20210811:45:58 AMef_minus +##contig= +##ALT= +##ALT= +##ALT= +##ALT= +##ALT= +##ALT= +##FILTER= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##FORMAT= +##FORMAT= +##FORMAT= +#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT promoterbamfilt/55492_f.bam +chr20 4685224 0 TTTTTTTTTTT N . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4685236;STD_quant_start=0.316228;STD_quant_stop=1.449138;Kurtosis_quant_start=3.075566;Kurtosis_quant_stop=1.117623;SVTYPE=DEL;SUPTYPE=AL;SVLEN=-12;STRANDS=+-;STRANDS2=12,2,12,2;RE=14;REF_strand=414,157;Strandbias_pval=0.37085;AF=0.0245184 GT:DR:DV 0/0:557:14 diff --git a/SVs_sniffles/vcf/55826_bodySnif.vcf b/SVs_sniffles/vcf/55826_bodySnif.vcf new file mode 100644 index 0000000..4c2c6f6 --- /dev/null +++ b/SVs_sniffles/vcf/55826_bodySnif.vcf @@ -0,0 +1,38 @@ +##fileformat=VCFv4.1 +##source=Sniffles +##fileDate=20210810:57:09 AMef_minus +##contig= +##ALT= +##ALT= +##ALT= +##ALT= +##ALT= +##ALT= +##FILTER= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##FORMAT= +##FORMAT= +##FORMAT= +#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT bamfilt/55826_f.bam +chr20 4698298 0 N CTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCCCCCCCCCCCCCCCCCCCCC . PASS IMPRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4698312;STD_quant_start=21.780152;STD_quant_stop=21.368786;Kurtosis_quant_start=-1.536178;Kurtosis_quant_stop=0.467587;SVTYPE=INS;SUPTYPE=AL;SVLEN=37;STRANDS=+-;STRANDS2=5,3,5,3;RE=8;REF_strand=6198,5806;Strandbias_pval=0.727647;AF=0.000666445 GT:DR:DV 0/0:11996:8 +chr20 4699449 1 CATGGTGGTGGCTGGGGACAGCCT N . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4699473;STD_quant_start=0.000000;STD_quant_stop=0.000000;Kurtosis_quant_start=3.557044;Kurtosis_quant_stop=3.843474;SVTYPE=DEL;SUPTYPE=AL;SVLEN=-24;STRANDS=+-;STRANDS2=1334,1291,1334,1291;RE=2625;REF_strand=6198,5806;Strandbias_pval=0.450664;AF=0.218677 GT:DR:DV 0/0:9379:2625 diff --git a/SVs_sniffles/vcf/55826_promoterSnif.vcf b/SVs_sniffles/vcf/55826_promoterSnif.vcf new file mode 100644 index 0000000..b9a1c72 --- /dev/null +++ b/SVs_sniffles/vcf/55826_promoterSnif.vcf @@ -0,0 +1,97 @@ +##fileformat=VCFv4.1 +##source=Sniffles +##fileDate=20210811:45:58 AMef_minus +##contig= +##ALT= +##ALT= +##ALT= +##ALT= +##ALT= +##ALT= +##FILTER= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##FORMAT= +##FORMAT= +##FORMAT= +#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT promoterbamfilt/55826_f.bam +chr20 4685224 0 GCCTCAGCTTTTTTTTTTT N . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4685235;STD_quant_start=0.000000;STD_quant_stop=1.060500;Kurtosis_quant_start=4.529223;Kurtosis_quant_stop=4.908722;SVTYPE=DEL;SUPTYPE=AL,NR;SVLEN=-11;STRANDS=+-;STRANDS2=393,346,393,346;RE=739;REF_strand=91979,72244;Strandbias_pval=0.127835;AF=0.00449998 GT:DR:DV 0/0:163484:739 +chr20 4685224 1 N TTTTTTTTTTTTTTTTTTT . STRANDBIAS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4685224;STD_quant_start=0.000000;STD_quant_stop=1.405187;Kurtosis_quant_start=51.212322;Kurtosis_quant_stop=1.984415;SVTYPE=INS;SUPTYPE=AL;SVLEN=11;STRANDS=+-;STRANDS2=4500,59,4500,59;RE=4559;REF_strand=91978,72208;Strandbias_pval=0;AF=0.0277673 GT:DR:DV 0/0:159627:4559 +chr20 4685223 2 TTTTTTTTTTTTTGTAAAGAGACAAAGAGTGAGA N . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4685262;STD_quant_start=3.033150;STD_quant_stop=9.402127;Kurtosis_quant_start=1.755029;Kurtosis_quant_stop=-0.850915;SVTYPE=DEL;SUPTYPE=AL,NR;SVLEN=-39;STRANDS=+-;STRANDS2=4,10,4,10;RE=14;REF_strand=91984,72294;Strandbias_pval=0.0564683;AF=8.52214e-05 GT:DR:DV 0/0:164264:14 +chr20 4685245 3 AGAGACAAAGAGTGAGACAGGG N . STRANDBIAS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4685266;STD_quant_start=6.843068;STD_quant_stop=7.353160;Kurtosis_quant_start=-1.848202;Kurtosis_quant_stop=-1.334587;SVTYPE=DEL;SUPTYPE=AL;SVLEN=-21;STRANDS=+-;STRANDS2=15,43,15,43;RE=58;REF_strand=91987,72372;Strandbias_pval=4.0455e-06;AF=0.000352886 GT:DR:DV 0/0:164301:58 +chr20 4685341 4 TCAAGCAATCCTCCCAT N . STRANDBIAS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4685361;STD_quant_start=3.890548;STD_quant_stop=2.931025;Kurtosis_quant_start=-0.552919;Kurtosis_quant_stop=0.000172;SVTYPE=DEL;SUPTYPE=AL;SVLEN=-20;STRANDS=+-;STRANDS2=14,30,14,30;RE=44;REF_strand=92032,72612;Strandbias_pval=0.00201075;AF=0.000267243 GT:DR:DV 0/0:164600:44 +chr20 4685413 5 N TTTTTGTTTTTTTTTTTTTTTTTTTTTTTTTTTTT . STRANDBIAS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4685414;STD_quant_start=0.000000;STD_quant_stop=2.004994;Kurtosis_quant_start=1.974642;Kurtosis_quant_stop=-0.960467;SVTYPE=INS;SUPTYPE=AL;SVLEN=11;STRANDS=+-;STRANDS2=86,15,86,15;RE=101;REF_strand=92038,72779;Strandbias_pval=5.1979e-10;AF=0.000612801 GT:DR:DV 0/0:164716:101 +chr20 4685422 6 N TTTTTTTTTTTTTT . STRANDBIAS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4685424;STD_quant_start=0.928477;STD_quant_stop=3.828207;Kurtosis_quant_start=-0.588901;Kurtosis_quant_stop=-1.186936;SVTYPE=INS;SUPTYPE=AL;SVLEN=12;STRANDS=+-;STRANDS2=43,16,43,16;RE=59;REF_strand=92038,72816;Strandbias_pval=0.00847086;AF=0.000357892 GT:DR:DV 0/0:164795:59 +chr20 4685486 7 TCTTCCTGCCTTGGCCTC N . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4685503;STD_quant_start=7.099296;STD_quant_stop=6.778643;Kurtosis_quant_start=-1.769799;Kurtosis_quant_stop=-1.794532;SVTYPE=DEL;SUPTYPE=AL;SVLEN=-17;STRANDS=+-;STRANDS2=24,17,24,17;RE=41;REF_strand=92038,73014;Strandbias_pval=0.755618;AF=0.000248407 GT:DR:DV 0/0:165011:41 +chr20 4685524 8 CCTGAGCCACTGCAC N . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4685541;STD_quant_start=7.874008;STD_quant_stop=7.444237;Kurtosis_quant_start=-2.124491;Kurtosis_quant_stop=-2.075067;SVTYPE=DEL;SUPTYPE=AL;SVLEN=-17;STRANDS=+-;STRANDS2=10,15,10,15;RE=25;REF_strand=92038,73090;Strandbias_pval=0.157348;AF=0.000151398 GT:DR:DV 0/0:165103:25 +chr20 4685537 9 N CGCAGCCGCAGCGGCAG . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4685551;STD_quant_start=8.436932;STD_quant_stop=8.528029;Kurtosis_quant_start=-2.051362;Kurtosis_quant_stop=-1.905650;SVTYPE=INS;SUPTYPE=AL;SVLEN=12;STRANDS=+-;STRANDS2=16,7,16,7;RE=23;REF_strand=92038,73113;Strandbias_pval=0.211678;AF=0.000139266 GT:DR:DV 0/0:165128:23 +chr20 4685579 10 TTCCTAAACCT N . PASS IMPRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4685601;STD_quant_start=10.302103;STD_quant_stop=10.567245;Kurtosis_quant_start=-2.062616;Kurtosis_quant_stop=-1.867756;SVTYPE=DEL;SUPTYPE=AL;SVLEN=-22;STRANDS=+-;STRANDS2=37,23,37,23;RE=60;REF_strand=92038,73216;Strandbias_pval=0.366433;AF=0.000363077 GT:DR:DV 0/0:165194:60 +chr20 4685633 11 N ACTTTTCTATCTCAA . PASS IMPRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4685648;STD_quant_start=11.040330;STD_quant_stop=12.249717;Kurtosis_quant_start=-1.814989;Kurtosis_quant_stop=-2.001355;SVTYPE=INS;SUPTYPE=AL;SVLEN=12;STRANDS=+-;STRANDS2=20,16,20,16;RE=36;REF_strand=92038,73338;Strandbias_pval=1;AF=0.000217686 GT:DR:DV 0/0:165340:36 +chr20 4685710 12 AATCCTGTCCTTCTATCACTTCATCC N . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4685738;STD_quant_start=9.848858;STD_quant_stop=4.219005;Kurtosis_quant_start=-0.341197;Kurtosis_quant_stop=-1.518409;SVTYPE=DEL;SUPTYPE=AL,NR;SVLEN=-28;STRANDS=+-;STRANDS2=12,4,12,4;RE=16;REF_strand=92038,73547;Strandbias_pval=0.136821;AF=9.66271e-05 GT:DR:DV 0/0:165569:16 +chr20 4685719 13 N CTTCTATTATTGCTG . PASS IMPRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4685736;STD_quant_start=12.617448;STD_quant_stop=10.835128;Kurtosis_quant_start=-1.424588;Kurtosis_quant_stop=-1.528312;SVTYPE=INS;SUPTYPE=AL;SVLEN=11;STRANDS=+-;STRANDS2=10,6,10,6;RE=16;REF_strand=92038,73557;Strandbias_pval=0.624762;AF=9.66213e-05 GT:DR:DV 0/0:165579:16 +chr20 4685777 14 CCACCCTGTTT N . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4685800;STD_quant_start=8.228446;STD_quant_stop=8.568234;Kurtosis_quant_start=-1.842431;Kurtosis_quant_stop=-1.831108;SVTYPE=DEL;SUPTYPE=AL;SVLEN=-23;STRANDS=+-;STRANDS2=42,41,42,41;RE=83;REF_strand=92038,73699;Strandbias_pval=0.378491;AF=0.000500793 GT:DR:DV 0/0:165654:83 +chr20 4685835 15 N CACATTAATATGGAATATTATAGAATAATAT . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4685859;STD_quant_start=7.253646;STD_quant_stop=5.442002;Kurtosis_quant_start=-1.968267;Kurtosis_quant_stop=-1.987889;SVTYPE=INS;SUPTYPE=AL;SVLEN=22;STRANDS=+-;STRANDS2=20,7,20,7;RE=27;REF_strand=92037,73819;Strandbias_pval=0.0547398;AF=0.000162792 GT:DR:DV 0/0:165829:27 +chr20 4685912 16 N GAGAGAAGGGAG . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4685920;STD_quant_start=8.578073;STD_quant_stop=9.146948;Kurtosis_quant_start=-1.408683;Kurtosis_quant_stop=-1.684252;SVTYPE=INS;SUPTYPE=AL;SVLEN=11;STRANDS=+-;STRANDS2=15,9,15,9;RE=24;REF_strand=92035,73964;Strandbias_pval=0.542953;AF=0.000144579 GT:DR:DV 0/0:165975:24 +chr20 4685982 17 AATTCATAAATATT N . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4685998;STD_quant_start=5.128353;STD_quant_stop=4.701064;Kurtosis_quant_start=-0.445254;Kurtosis_quant_stop=-1.179100;SVTYPE=DEL;SUPTYPE=AL,NR;SVLEN=-16;STRANDS=+-;STRANDS2=6,10,6,10;RE=16;REF_strand=91861,74184;Strandbias_pval=0.208161;AF=9.63594e-05 GT:DR:DV 0/0:166029:16 +chr20 4686021 18 N TTTTTTTTTTT . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4686024;STD_quant_start=1.549193;STD_quant_stop=2.302173;Kurtosis_quant_start=-0.894123;Kurtosis_quant_stop=-1.687007;SVTYPE=INS;SUPTYPE=AL;SVLEN=11;STRANDS=+-;STRANDS2=13,8,13,8;RE=21;REF_strand=91695,74296;Strandbias_pval=0.662477;AF=0.000126513 GT:DR:DV 0/0:165970:21 +chr20 4686077 19 TCATTCCTGAGCCTT N . STRANDBIAS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4686091;STD_quant_start=1.414214;STD_quant_stop=1.367320;Kurtosis_quant_start=-0.343287;Kurtosis_quant_stop=1.675565;SVTYPE=DEL;SUPTYPE=AL,NR;SVLEN=-14;STRANDS=+-;STRANDS2=39,8,39,8;RE=47;REF_strand=91324,74460;Strandbias_pval=9.16652e-05;AF=0.000283501 GT:DR:DV 0/0:165737:47 +chr20 4686019 20 AAAATTTTTTGCTCTCCTCTTT N . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4686040;STD_quant_start=4.511097;STD_quant_stop=7.169379;Kurtosis_quant_start=-1.695838;Kurtosis_quant_stop=-2.014979;SVTYPE=DEL;SUPTYPE=AL;SVLEN=-21;STRANDS=+-;STRANDS2=16,24,16,24;RE=40;REF_strand=91641,74311;Strandbias_pval=0.0572517;AF=0.000241034 GT:DR:DV 0/0:165912:40 +chr20 4686086 21 N CTCTCTTTCGCTT . PASS IMPRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4686099;STD_quant_start=11.009087;STD_quant_stop=11.189281;Kurtosis_quant_start=-1.917138;Kurtosis_quant_stop=-1.832618;SVTYPE=INS;SUPTYPE=AL;SVLEN=11;STRANDS=+-;STRANDS2=12,6,12,6;RE=18;REF_strand=91292,74477;Strandbias_pval=0.354308;AF=0.000108585 GT:DR:DV 0/0:165751:18 +chr20 4686047 22 TTTCTGGTTGCCAAAGTTC N . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4686063;STD_quant_start=4.549725;STD_quant_stop=5.603570;Kurtosis_quant_start=-0.667954;Kurtosis_quant_stop=-0.773469;SVTYPE=DEL;SUPTYPE=AL;SVLEN=-16;STRANDS=+-;STRANDS2=6,9,6,9;RE=15;REF_strand=91485,74387;Strandbias_pval=0.301352;AF=9.04312e-05 GT:DR:DV 0/0:165857:15 +chr20 4686162 23 N TTTTTTTTTTTTTTTT . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4686167;STD_quant_start=0.000000;STD_quant_stop=3.717282;Kurtosis_quant_start=-0.977092;Kurtosis_quant_stop=-1.038613;SVTYPE=INS;SUPTYPE=AL;SVLEN=11;STRANDS=+-;STRANDS2=16,7,16,7;RE=23;REF_strand=90937,74642;Strandbias_pval=0.208668;AF=0.000138907 GT:DR:DV 0/0:165556:23 +chr20 4686196 24 GGCACCCGCAG N . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4686209;STD_quant_start=4.062019;STD_quant_stop=2.017778;Kurtosis_quant_start=-1.448033;Kurtosis_quant_stop=-1.257707;SVTYPE=DEL;SUPTYPE=AL;SVLEN=-13;STRANDS=+-;STRANDS2=19,10,19,10;RE=29;REF_strand=90733,74781;Strandbias_pval=0.26861;AF=0.000175212 GT:DR:DV 0/0:165485:29 +chr20 4686230 25 CAAGCGAATCTC N . STRANDBIAS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4686243;STD_quant_start=3.175426;STD_quant_stop=5.000000;Kurtosis_quant_start=0.501373;Kurtosis_quant_stop=0.389479;SVTYPE=DEL;SUPTYPE=AL;SVLEN=-13;STRANDS=+-;STRANDS2=6,19,6,19;RE=25;REF_strand=90552,74874;Strandbias_pval=0.00222641;AF=0.000151125 GT:DR:DV 0/0:165401:25 +chr20 4686248 26 N TTTTTTTTTTTTTTT . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4686250;STD_quant_start=3.391165;STD_quant_stop=3.674235;Kurtosis_quant_start=-0.644471;Kurtosis_quant_stop=-0.349761;SVTYPE=INS;SUPTYPE=AL;SVLEN=12;STRANDS=+-;STRANDS2=17,4,17,4;RE=21;REF_strand=90457,74914;Strandbias_pval=0.0157991;AF=0.000126987 GT:DR:DV 0/0:165350:21 +chr20 4686262 27 CATTCCCGGCCCTG N . PASS IMPRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4686304;STD_quant_start=10.909887;STD_quant_stop=5.479566;Kurtosis_quant_start=-2.080097;Kurtosis_quant_stop=-1.571270;SVTYPE=DEL;SUPTYPE=AL;SVLEN=-42;STRANDS=+-;STRANDS2=43,35,43,35;RE=78;REF_strand=90243,75007;Strandbias_pval=1;AF=0.000472012 GT:DR:DV 0/0:165172:78 +chr20 4686319 28 N GGTGGCACGCCGCCTT . PASS IMPRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4686328;STD_quant_start=10.748461;STD_quant_stop=11.507031;Kurtosis_quant_start=-2.022324;Kurtosis_quant_stop=-1.928829;SVTYPE=INS;SUPTYPE=AL;SVLEN=12;STRANDS=+-;STRANDS2=20,14,20,14;RE=34;REF_strand=89993,75119;Strandbias_pval=0.731172;AF=0.000205921 GT:DR:DV 0/0:165078:34 +chr20 4686310 29 GGCACAGAGTGTGCGCCGGGCC N . STRANDBIAS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4686351;STD_quant_start=9.223081;STD_quant_stop=6.277981;Kurtosis_quant_start=-2.013562;Kurtosis_quant_stop=-1.497925;SVTYPE=DEL;SUPTYPE=AL;SVLEN=-41;STRANDS=+-;STRANDS2=23,69,23,69;RE=92;REF_strand=89949,75173;Strandbias_pval=1.17269e-08;AF=0.000557164 GT:DR:DV 0/0:165030:92 +chr20 4686392 30 CCCCGCGTCCCT N . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4686403;STD_quant_start=5.094421;STD_quant_stop=4.723611;Kurtosis_quant_start=-1.658842;Kurtosis_quant_stop=-1.537860;SVTYPE=DEL;SUPTYPE=AL;SVLEN=-11;STRANDS=+-;STRANDS2=62,66,62,66;RE=128;REF_strand=89565,75399;Strandbias_pval=0.184551;AF=0.000775927 GT:DR:DV 0/0:164836:128 +chr20 4686416 31 CGTCCCTCCCC N . STRANDBIAS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4686427;STD_quant_start=3.623994;STD_quant_stop=3.069564;Kurtosis_quant_start=0.294556;Kurtosis_quant_stop=0.985845;SVTYPE=DEL;SUPTYPE=AL;SVLEN=-11;STRANDS=+-;STRANDS2=25,66,25,66;RE=91;REF_strand=89440,75466;Strandbias_pval=4.08402e-07;AF=0.00055183 GT:DR:DV 0/0:164815:91 +chr20 4686438 32 N GCCTTCTTGCCT . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4686446;STD_quant_start=9.721111;STD_quant_stop=9.196920;Kurtosis_quant_start=-1.934848;Kurtosis_quant_stop=-1.708794;SVTYPE=INS;SUPTYPE=AL;SVLEN=12;STRANDS=+-;STRANDS2=14,10,14,10;RE=24;REF_strand=89363,75536;Strandbias_pval=0.838262;AF=0.000145544 GT:DR:DV 0/0:164875:24 +chr20 4686486 33 CTTCTCCTCTC N . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4686497;STD_quant_start=3.484141;STD_quant_stop=3.471402;Kurtosis_quant_start=-1.113201;Kurtosis_quant_stop=-1.301940;SVTYPE=DEL;SUPTYPE=AL;SVLEN=-11;STRANDS=+-;STRANDS2=74,84,74,84;RE=158;REF_strand=89148,75669;Strandbias_pval=0.0786037;AF=0.000958639 GT:DR:DV 0/0:164659:158 +chr20 4686509 34 N CGCGGCGCGGCAGC . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4686518;STD_quant_start=4.427189;STD_quant_stop=5.848077;Kurtosis_quant_start=-1.061033;Kurtosis_quant_stop=-1.312116;SVTYPE=INS;SUPTYPE=AL;SVLEN=11;STRANDS=+-;STRANDS2=9,9,9,9;RE=18;REF_strand=89055,75740;Strandbias_pval=0.814957;AF=0.000109227 GT:DR:DV 0/0:164777:18 +chr20 4686522 35 GGGTGGGAGGAACGCGGGC N . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4686547;STD_quant_start=1.702939;STD_quant_stop=8.087027;Kurtosis_quant_start=1.161333;Kurtosis_quant_stop=-0.559743;SVTYPE=DEL;SUPTYPE=AL;SVLEN=-25;STRANDS=+-;STRANDS2=5,11,5,11;RE=16;REF_strand=88837,75813;Strandbias_pval=0.0810501;AF=9.71758e-05 GT:DR:DV 0/0:164634:16 +chr20 4686566 36 N CCAACACGAGACGCCGCAAGACAGC . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4686577;STD_quant_start=4.615192;STD_quant_stop=8.360622;Kurtosis_quant_start=-1.071456;Kurtosis_quant_stop=-0.806682;SVTYPE=INS;SUPTYPE=AL;SVLEN=11;STRANDS=+-;STRANDS2=7,9,7,9;RE=16;REF_strand=88616,75957;Strandbias_pval=0.459896;AF=9.72213e-05 GT:DR:DV 0/0:164557:16 +chr20 4686623 37 N CGCGCCCGCTACAG . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4686626;STD_quant_start=6.575011;STD_quant_stop=3.892794;Kurtosis_quant_start=-1.355958;Kurtosis_quant_stop=-0.764406;SVTYPE=INS;SUPTYPE=AL;SVLEN=12;STRANDS=+-;STRANDS2=18,8,18,8;RE=26;REF_strand=88452,76184;Strandbias_pval=0.120352;AF=0.000157924 GT:DR:DV 0/0:164610:26 +chr20 4686637 38 GGAGGGGCCGGG N . STRANDBIAS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4686649;STD_quant_start=3.211204;STD_quant_stop=3.584615;Kurtosis_quant_start=-1.429511;Kurtosis_quant_stop=-1.362664;SVTYPE=DEL;SUPTYPE=AL;SVLEN=-12;STRANDS=+-;STRANDS2=61,126,61,126;RE=187;REF_strand=88388,76238;Strandbias_pval=9.89633e-09;AF=0.00113591 GT:DR:DV 0/0:164439:187 +chr20 4686720 39 GTTGGGGGGCTGGGGGAGCTG N . PASS IMPRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4686779;STD_quant_start=11.330637;STD_quant_stop=16.804761;Kurtosis_quant_start=-1.914197;Kurtosis_quant_stop=-1.893270;SVTYPE=DEL;SUPTYPE=AL;SVLEN=-59;STRANDS=+-;STRANDS2=55,65,55,65;RE=120;REF_strand=87908,76609;Strandbias_pval=0.0998487;AF=0.000729408 GT:DR:DV 0/0:164397:120 +chr20 4686891 40 GGGCCGCCAGCG N . STRANDBIAS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4686902;STD_quant_start=2.758824;STD_quant_stop=1.885618;Kurtosis_quant_start=-0.894586;Kurtosis_quant_stop=-0.031248;SVTYPE=DEL;SUPTYPE=AL,NR;SVLEN=-11;STRANDS=+-;STRANDS2=11,26,11,26;RE=37;REF_strand=87261,77133;Strandbias_pval=0.00481682;AF=0.000225069 GT:DR:DV 0/0:164357:37 +chr20 4686973 41 GCCCAGAACGCC N . PASS IMPRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4687008;STD_quant_start=13.272779;STD_quant_stop=3.696846;Kurtosis_quant_start=-1.869527;Kurtosis_quant_stop=-1.391686;SVTYPE=DEL;SUPTYPE=AL;SVLEN=-35;STRANDS=+-;STRANDS2=18,18,18,18;RE=36;REF_strand=86824,77554;Strandbias_pval=0.741859;AF=0.000219007 GT:DR:DV 0/0:164342:36 +chr20 4686974 42 N GTCAAAGGAGA . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4686987;STD_quant_start=7.009517;STD_quant_stop=8.744522;Kurtosis_quant_start=-1.570112;Kurtosis_quant_stop=-1.957945;SVTYPE=INS;SUPTYPE=AL;SVLEN=11;STRANDS=+-;STRANDS2=18,13,18,13;RE=31;REF_strand=86869,77509;Strandbias_pval=0.594057;AF=0.00018859 GT:DR:DV 0/0:164347:31 +chr20 4687066 43 GGGGCGCCCGCCGGG N . STRANDBIAS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4687087;STD_quant_start=6.937313;STD_quant_stop=7.881357;Kurtosis_quant_start=-1.219226;Kurtosis_quant_stop=-1.228356;SVTYPE=DEL;SUPTYPE=AL;SVLEN=-21;STRANDS=+-;STRANDS2=63,127,63,127;RE=190;REF_strand=86500,77849;Strandbias_pval=7.92999e-08;AF=0.00115608 GT:DR:DV 0/0:164159:190 +chr20 4687109 44 CCGCAGCTGCAGCGTT N . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4687125;STD_quant_start=5.162736;STD_quant_stop=5.522681;Kurtosis_quant_start=-1.192007;Kurtosis_quant_stop=-0.694359;SVTYPE=DEL;SUPTYPE=AL;SVLEN=-16;STRANDS=+-;STRANDS2=32,21,32,21;RE=53;REF_strand=86341,78007;Strandbias_pval=0.273323;AF=0.000322486 GT:DR:DV 0/0:164295:53 +chr20 4687122 45 N GTGTGCGGCACT . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4687126;STD_quant_start=6.480741;STD_quant_stop=4.929503;Kurtosis_quant_start=-2.040849;Kurtosis_quant_stop=-1.904245;SVTYPE=INS;SUPTYPE=AL;SVLEN=11;STRANDS=+-;STRANDS2=7,14,7,14;RE=21;REF_strand=86306,78032;Strandbias_pval=0.08452;AF=0.000127785 GT:DR:DV 0/0:164317:21 +chr20 4687166 46 GCTTCTCCGAG N . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4687177;STD_quant_start=5.513620;STD_quant_stop=4.478520;Kurtosis_quant_start=-1.819972;Kurtosis_quant_stop=-1.648264;SVTYPE=DEL;SUPTYPE=AL;SVLEN=-11;STRANDS=+-;STRANDS2=33,37,33,37;RE=70;REF_strand=86206,78154;Strandbias_pval=0.403254;AF=0.000425894 GT:DR:DV 0/0:164290:70 +chr20 4687178 47 GGGGCTGCAGCCTTGCGGCCGTTGCCA N . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4687204;STD_quant_start=7.606112;STD_quant_stop=6.840623;Kurtosis_quant_start=-1.315374;Kurtosis_quant_stop=-0.970706;SVTYPE=DEL;SUPTYPE=AL;SVLEN=-26;STRANDS=+-;STRANDS2=40,28,40,28;RE=68;REF_strand=86140,78157;Strandbias_pval=0.331755;AF=0.000413885 GT:DR:DV 0/0:164229:68 +chr20 4687243 48 N GAAGGAGAAGG . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4687244;STD_quant_start=8.485281;STD_quant_stop=8.831761;Kurtosis_quant_start=-1.972572;Kurtosis_quant_stop=-1.777312;SVTYPE=INS;SUPTYPE=AL;SVLEN=15;STRANDS=+-;STRANDS2=10,12,10,12;RE=22;REF_strand=85939,78158;Strandbias_pval=0.530655;AF=0.000134067 GT:DR:DV 0/0:164075:22 +chr20 4687355 49 CGGACCCCAGC N . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4687366;STD_quant_start=3.783186;STD_quant_stop=3.391165;Kurtosis_quant_start=-1.386782;Kurtosis_quant_stop=-1.613489;SVTYPE=DEL;SUPTYPE=AL;SVLEN=-11;STRANDS=+-;STRANDS2=22,11,22,11;RE=33;REF_strand=85442,78158;Strandbias_pval=0.116721;AF=0.000201711 GT:DR:DV 0/0:163567:33 +chr20 4687394 50 N GCACTGCGCCTGT . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4687399;STD_quant_start=7.035624;STD_quant_stop=7.266361;Kurtosis_quant_start=-0.078746;Kurtosis_quant_stop=-0.950028;SVTYPE=INS;SUPTYPE=AL;SVLEN=17;STRANDS=+-;STRANDS2=5,8,5,8;RE=13;REF_strand=85342,78158;Strandbias_pval=0.408852;AF=7.95107e-05 GT:DR:DV 0/0:163487:13 +chr20 4687452 51 CCCTTGGGTCACCGGTCTCC N . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4687472;STD_quant_start=4.266146;STD_quant_stop=7.127412;Kurtosis_quant_start=0.321781;Kurtosis_quant_stop=0.340044;SVTYPE=DEL;SUPTYPE=AL;SVLEN=-20;STRANDS=+-;STRANDS2=6,9,6,9;RE=15;REF_strand=85182,78158;Strandbias_pval=0.440887;AF=9.1833e-05 GT:DR:DV 0/0:163325:15 +chr20 4687590 52 N TTTTTTTTTTT . STRANDBIAS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4687590;STD_quant_start=0.000000;STD_quant_stop=2.586289;Kurtosis_quant_start=1.547707;Kurtosis_quant_stop=-0.378996;SVTYPE=INS;SUPTYPE=AL;SVLEN=11;STRANDS=+-;STRANDS2=85,6,85,6;RE=91;REF_strand=84720,78158;Strandbias_pval=8.24942e-18;AF=0.0005587 GT:DR:DV 0/0:162787:91 +chr20 4687581 53 TTTTTTTTTAAC N . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4687603;STD_quant_start=6.989210;STD_quant_stop=8.300943;Kurtosis_quant_start=-1.506631;Kurtosis_quant_stop=-1.791213;SVTYPE=DEL;SUPTYPE=AL,NR;SVLEN=-22;STRANDS=+-;STRANDS2=55,51,55,51;RE=106;REF_strand=84736,78158;Strandbias_pval=1;AF=0.00065073 GT:DR:DV 0/0:162788:106 +chr20 4687656 54 TCCGTTTTTGTT N . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4687669;STD_quant_start=2.900304;STD_quant_stop=1.970369;Kurtosis_quant_start=0.989411;Kurtosis_quant_stop=0.568773;SVTYPE=DEL;SUPTYPE=AL;SVLEN=-13;STRANDS=+-;STRANDS2=14,20,14,20;RE=34;REF_strand=84564,78158;Strandbias_pval=0.231885;AF=0.000208945 GT:DR:DV 0/0:162688:34 +chr20 4687669 55 CCAGATTCTCACACAAC N . STRANDBIAS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4687692;STD_quant_start=4.857983;STD_quant_stop=3.391165;Kurtosis_quant_start=-1.467398;Kurtosis_quant_stop=1.227961;SVTYPE=DEL;SUPTYPE=AL;SVLEN=-23;STRANDS=+-;STRANDS2=2,17,2,17;RE=19;REF_strand=84509,78158;Strandbias_pval=0.00027153;AF=0.000116803 GT:DR:DV 0/0:162648:19 +chr20 4687726 56 TTCATGGCCGCG N . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4687740;STD_quant_start=7.798751;STD_quant_stop=7.719439;Kurtosis_quant_start=-1.915745;Kurtosis_quant_stop=-1.928893;SVTYPE=DEL;SUPTYPE=AL;SVLEN=-14;STRANDS=+-;STRANDS2=44,35,44,35;RE=79;REF_strand=84343,78158;Strandbias_pval=0.57366;AF=0.000486151 GT:DR:DV 0/0:162422:79 +chr20 4687778 57 CCCATATGATT N . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4687794;STD_quant_start=4.144451;STD_quant_stop=2.711631;Kurtosis_quant_start=-1.863511;Kurtosis_quant_stop=-1.909432;SVTYPE=DEL;SUPTYPE=AL;SVLEN=-16;STRANDS=+-;STRANDS2=11,24,11,24;RE=35;REF_strand=84195,78156;Strandbias_pval=0.0174786;AF=0.000215582 GT:DR:DV 0/0:162316:35 +chr20 4687867 58 N AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA . STRANDBIAS IMPRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4687914;STD_quant_start=24.232427;STD_quant_stop=11.792058;Kurtosis_quant_start=-2.092868;Kurtosis_quant_stop=-2.036282;SVTYPE=INS;SUPTYPE=AL;SVLEN=16;STRANDS=+-;STRANDS2=12,27,12,27;RE=39;REF_strand=83798,78152;Strandbias_pval=0.00988687;AF=0.000240815 GT:DR:DV 0/0:161911:39 +chr20 4687919 59 AAACTTCTGGAA N . PASS IMPRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4687940;STD_quant_start=10.612040;STD_quant_stop=10.473410;Kurtosis_quant_start=-2.139541;Kurtosis_quant_stop=-1.869549;SVTYPE=DEL;SUPTYPE=AL;SVLEN=-21;STRANDS=+-;STRANDS2=24,28,24,28;RE=52;REF_strand=83634,78142;Strandbias_pval=0.48831;AF=0.000321432 GT:DR:DV 0/0:161724:52 +chr20 4688011 60 N AAAAAAAAAAAAAA . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4688015;STD_quant_start=0.000000;STD_quant_stop=1.568929;Kurtosis_quant_start=1.991647;Kurtosis_quant_stop=0.630460;SVTYPE=INS;SUPTYPE=AL;SVLEN=11;STRANDS=+-;STRANDS2=7,19,7,19;RE=26;REF_strand=82886,77932;Strandbias_pval=0.0168909;AF=0.000161673 GT:DR:DV 0/0:160792:26 diff --git a/SVs_sniffles/vcf/56635_bodySnif.vcf b/SVs_sniffles/vcf/56635_bodySnif.vcf new file mode 100644 index 0000000..519a742 --- /dev/null +++ b/SVs_sniffles/vcf/56635_bodySnif.vcf @@ -0,0 +1,39 @@ +##fileformat=VCFv4.1 +##source=Sniffles +##fileDate=20210810:57:30 AMef_minus +##contig= +##ALT= +##ALT= +##ALT= +##ALT= +##ALT= +##ALT= +##FILTER= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##FORMAT= +##FORMAT= +##FORMAT= +#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT bamfilt/56635_f.bam +chr20 4689780 0 N TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4689805;STD_quant_start=5.049752;STD_quant_stop=6.123724;Kurtosis_quant_start=-1.514564;Kurtosis_quant_stop=-1.362808;SVTYPE=INS;SUPTYPE=AL;SVLEN=28;STRANDS=+-;STRANDS2=15,5,15,5;RE=20;REF_strand=26644,26994;Strandbias_pval=0.0256971;AF=0.00037287 GT:DR:DV 0/0:53618:20 +chr20 4692347 1 N GGACTCACTGAGTTTCCTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTGGATTTCCCCCCCCCCCCC . PASS IMPRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4692347;STD_quant_start=17.606817;STD_quant_stop=16.397832;Kurtosis_quant_start=4.836011;Kurtosis_quant_stop=1.333899;SVTYPE=INS;SUPTYPE=AL;SVLEN=74;STRANDS=+-;STRANDS2=4,5,4,5;RE=9;REF_strand=26704,27030;Strandbias_pval=1;AF=0.000167492 GT:DR:DV 0/0:53725:9 +chr20 4701259 2 N AAAAAAAAAAAAAAAAAAAAAAAAAATATATAT . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4701263;STD_quant_start=6.276942;STD_quant_stop=7.314369;Kurtosis_quant_start=-0.697081;Kurtosis_quant_stop=-0.450266;SVTYPE=INS;SUPTYPE=AL;SVLEN=33;STRANDS=+-;STRANDS2=5,11,5,11;RE=16;REF_strand=26676,27018;Strandbias_pval=0.210199;AF=0.000297985 GT:DR:DV 0/0:53678:16 diff --git a/SVs_sniffles/vcf/56635_promoterSnif.vcf b/SVs_sniffles/vcf/56635_promoterSnif.vcf new file mode 100644 index 0000000..15ae77b --- /dev/null +++ b/SVs_sniffles/vcf/56635_promoterSnif.vcf @@ -0,0 +1,124 @@ +##fileformat=VCFv4.1 +##source=Sniffles +##fileDate=20210811:47:24 AMef_minus +##contig= +##ALT= +##ALT= +##ALT= +##ALT= +##ALT= +##ALT= +##FILTER= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##FORMAT= +##FORMAT= +##FORMAT= +#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT promoterbamfilt/56635_f.bam +chr20 4685155 0 N AAAAAAAAAAAAAAAT . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4685158;STD_quant_start=5.949790;STD_quant_stop=6.542171;Kurtosis_quant_start=-1.559305;Kurtosis_quant_stop=-1.525236;SVTYPE=INS;SUPTYPE=AL;SVLEN=11;STRANDS=+-;STRANDS2=10,8,10,8;RE=18;REF_strand=226534,166140;Strandbias_pval=1;AF=4.58396e-05 GT:DR:DV 0/0:392656:18 +chr20 4685137 1 TGTACCCCTCC N . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4685161;STD_quant_start=5.800702;STD_quant_stop=7.540017;Kurtosis_quant_start=-1.836605;Kurtosis_quant_stop=-0.588717;SVTYPE=DEL;SUPTYPE=AL;SVLEN=-24;STRANDS=+-;STRANDS2=126,90,126,90;RE=216;REF_strand=226507,166078;Strandbias_pval=0.890508;AF=0.000550199 GT:DR:DV 0/0:392369:216 +chr20 4685224 2 TTTTTTTTTTT N . STRANDBIAS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4685235;STD_quant_start=0.000000;STD_quant_stop=1.463641;Kurtosis_quant_start=2.310904;Kurtosis_quant_stop=1.985544;SVTYPE=DEL;SUPTYPE=AL,NR;SVLEN=-11;STRANDS=+-;STRANDS2=989,881,989,881;RE=1870;REF_strand=226591,166605;Strandbias_pval=4.0066e-05;AF=0.0047559 GT:DR:DV 0/0:391326:1870 +chr20 4685224 3 N TTTTTTTTTTT . STRANDBIAS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4685224;STD_quant_start=0.000000;STD_quant_stop=1.168450;Kurtosis_quant_start=42.686804;Kurtosis_quant_stop=1.799793;SVTYPE=INS;SUPTYPE=AL;SVLEN=11;STRANDS=+-;STRANDS2=6457,201,6457,201;RE=6658;REF_strand=226586,166564;Strandbias_pval=0;AF=0.016935 GT:DR:DV 0/0:386492:6658 +chr20 4685224 4 TTTTTTTTTTTTTGTAAAGAGACAAAGAGTGAGACAGGGTCTTGGCCTATAGCCCTGTGGCCCA N . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4685290;STD_quant_start=0.774597;STD_quant_stop=7.234178;Kurtosis_quant_start=0.695824;Kurtosis_quant_stop=-1.046920;SVTYPE=DEL;SUPTYPE=AL,NR;SVLEN=-66;STRANDS=+-;STRANDS2=16,15,16,15;RE=31;REF_strand=226641,166825;Strandbias_pval=0.586424;AF=7.8787e-05 GT:DR:DV 0/0:393435:31 +chr20 4685293 5 N TCCTCCCTCCGTCTCCAGCAATG . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4685302;STD_quant_start=7.576279;STD_quant_stop=5.477226;Kurtosis_quant_start=-2.112498;Kurtosis_quant_stop=-1.681799;SVTYPE=INS;SUPTYPE=AL;SVLEN=11;STRANDS=+-;STRANDS2=8,11,8,11;RE=19;REF_strand=226698,167124;Strandbias_pval=0.245045;AF=4.82451e-05 GT:DR:DV 0/0:393803:19 +chr20 4685332 6 CAGCCTCTACCTCCTGGGCTCAAGCAATCCTCCCATCTCAGCCTCCCCAGTAGCTGGGACTACAGGACTGTGCCACCGTTCCCAGCAATTTTTTTTAT N . PASS IMPRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4685432;STD_quant_start=12.645157;STD_quant_stop=11.117554;Kurtosis_quant_start=-1.582060;Kurtosis_quant_stop=-0.880746;SVTYPE=DEL;SUPTYPE=AL;SVLEN=-100;STRANDS=+-;STRANDS2=9,4,9,4;RE=13;REF_strand=226708,167520;Strandbias_pval=0.576603;AF=3.29758e-05 GT:DR:DV 0/0:394215:13 +chr20 4685413 7 N TTTTTTTTTTTTTT . STRANDBIAS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4685413;STD_quant_start=0.000000;STD_quant_stop=1.324329;Kurtosis_quant_start=0.910756;Kurtosis_quant_stop=0.280201;SVTYPE=INS;SUPTYPE=AL;SVLEN=11;STRANDS=+-;STRANDS2=115,16,115,16;RE=131;REF_strand=226712,167652;Strandbias_pval=5.85099e-14;AF=0.00033218 GT:DR:DV 0/0:394233:131 +chr20 4685413 8 N TTTCCTTTTTTTTTTTTTTTTTT . STRANDBIAS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4685422;STD_quant_start=1.521991;STD_quant_stop=2.255794;Kurtosis_quant_start=-0.919673;Kurtosis_quant_stop=0.961825;SVTYPE=INS;SUPTYPE=AL;SVLEN=11;STRANDS=+-;STRANDS2=143,16,143,16;RE=159;REF_strand=226712,167674;Strandbias_pval=2.80784e-19;AF=0.000403158 GT:DR:DV 0/0:394227:159 +chr20 4685464 9 CTCAAACTCCTGAG N . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4685478;STD_quant_start=4.411929;STD_quant_stop=5.000000;Kurtosis_quant_start=-0.453794;Kurtosis_quant_stop=-0.742320;SVTYPE=DEL;SUPTYPE=AL;SVLEN=-14;STRANDS=+-;STRANDS2=52,34,52,34;RE=86;REF_strand=226716,167887;Strandbias_pval=0.587788;AF=0.000217941 GT:DR:DV 0/0:394517:86 +chr20 4685530 10 CTGAGCCACTGCACCTGGCTGTCAACATTCTTAAATCT N . PASS IMPRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4685572;STD_quant_start=4.760952;STD_quant_stop=11.944315;Kurtosis_quant_start=-1.038592;Kurtosis_quant_stop=-1.567594;SVTYPE=DEL;SUPTYPE=AL;SVLEN=-42;STRANDS=+-;STRANDS2=27,9,27,9;RE=36;REF_strand=226724,168242;Strandbias_pval=0.0417681;AF=9.11471e-05 GT:DR:DV 0/0:394930:36 +chr20 4685477 11 N CCCTCCTCTCCTTC . PASS IMPRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4685490;STD_quant_start=11.614419;STD_quant_stop=12.024099;Kurtosis_quant_start=-1.765192;Kurtosis_quant_stop=-1.998527;SVTYPE=INS;SUPTYPE=AL;SVLEN=11;STRANDS=+-;STRANDS2=26,12,26,12;RE=38;REF_strand=226717,167942;Strandbias_pval=0.191712;AF=9.62857e-05 GT:DR:DV 0/0:394621:38 +chr20 4685552 12 CATTCTTAAAT N . STRANDBIAS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4685563;STD_quant_start=5.744563;STD_quant_stop=5.975440;Kurtosis_quant_start=-1.743987;Kurtosis_quant_stop=-0.770300;SVTYPE=DEL;SUPTYPE=AL;SVLEN=-11;STRANDS=+-;STRANDS2=32,2,32,2;RE=34;REF_strand=226725,168277;Strandbias_pval=2.48194e-06;AF=8.60755e-05 GT:DR:DV 0/0:394968:34 +chr20 4685624 13 CCCCAGGGCATGCCTGGTTTACGCCCATTTCACTTTAAAAGTGCCCAATTTGGGTAATAATTTATAAGATCCCCCTCCCTCTAAATCCTGTCCTTCTATCACTTCATCCTTCGCTCTCCTTTAAAA N . STRANDBIAS IMPRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4685754;STD_quant_start=21.918029;STD_quant_stop=18.865312;Kurtosis_quant_start=-1.148733;Kurtosis_quant_stop=-1.430566;SVTYPE=DEL;SUPTYPE=AL,NR;SVLEN=-130;STRANDS=+-;STRANDS2=12,0,12,0;RE=12;REF_strand=226733,168819;Strandbias_pval=0.00188326;AF=3.03374e-05 GT:DR:DV 0/0:395540:12 +chr20 4685631 14 GGCATGCCTGGTTTACGCCCATTTCACTTTAAAAGTGCCC N . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4685675;STD_quant_start=9.513149;STD_quant_stop=6.363961;Kurtosis_quant_start=-1.863714;Kurtosis_quant_stop=-0.869251;SVTYPE=DEL;SUPTYPE=AL;SVLEN=-44;STRANDS=+-;STRANDS2=13,4,13,4;RE=17;REF_strand=226734,168638;Strandbias_pval=0.142371;AF=4.29975e-05 GT:DR:DV 0/0:395355:17 +chr20 4685693 15 ATCCCCCTCCC N . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4685709;STD_quant_start=6.167252;STD_quant_stop=6.501538;Kurtosis_quant_start=-1.729831;Kurtosis_quant_stop=-1.709970;SVTYPE=DEL;SUPTYPE=AL,NR;SVLEN=-16;STRANDS=+-;STRANDS2=227,174,227,174;RE=401;REF_strand=226734,168852;Strandbias_pval=0.800673;AF=0.00101369 GT:DR:DV 0/0:395185:401 +chr20 4685693 16 N GTAAGATCCCCCCCCCCTCC . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4685700;STD_quant_start=6.087327;STD_quant_stop=7.051399;Kurtosis_quant_start=-1.409634;Kurtosis_quant_stop=-1.233014;SVTYPE=INS;SUPTYPE=AL;SVLEN=13;STRANDS=+-;STRANDS2=24,13,24,13;RE=37;REF_strand=226734,168835;Strandbias_pval=0.40806;AF=9.35361e-05 GT:DR:DV 0/0:395532:37 +chr20 4685777 17 CGCAAGAACACAC N . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4685790;STD_quant_start=5.833455;STD_quant_stop=6.589086;Kurtosis_quant_start=-1.373566;Kurtosis_quant_stop=-1.503432;SVTYPE=DEL;SUPTYPE=AL,NR;SVLEN=-13;STRANDS=+-;STRANDS2=171,104,171,104;RE=275;REF_strand=226734,169209;Strandbias_pval=0.100146;AF=0.000694544 GT:DR:DV 0/0:395668:275 +chr20 4685835 18 N TTTTTTTTTTTT . STRANDBIAS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4685837;STD_quant_start=3.389058;STD_quant_stop=6.362839;Kurtosis_quant_start=-1.564122;Kurtosis_quant_stop=-1.577944;SVTYPE=INS;SUPTYPE=AL;SVLEN=11;STRANDS=+-;STRANDS2=56,15,56,15;RE=71;REF_strand=226734,169473;Strandbias_pval=0.000166381;AF=0.000179199 GT:DR:DV 0/0:396136:71 +chr20 4685859 19 N TCATTTAGCGGGCAT . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4685867;STD_quant_start=5.069517;STD_quant_stop=8.532292;Kurtosis_quant_start=0.604923;Kurtosis_quant_stop=-1.324086;SVTYPE=INS;SUPTYPE=AL;SVLEN=12;STRANDS=+-;STRANDS2=10,6,10,6;RE=16;REF_strand=226736,169597;Strandbias_pval=0.802721;AF=4.03701e-05 GT:DR:DV 0/0:396317:16 +chr20 4685850 20 TTTTTCTCATTTGTTAATATCACCACCTAAATCATCTCTTGCCTAAAACAAGGAGTAGAAAG N . PASS IMPRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4685914;STD_quant_start=12.401613;STD_quant_stop=9.354143;Kurtosis_quant_start=-1.096625;Kurtosis_quant_stop=-1.247839;SVTYPE=DEL;SUPTYPE=AL;SVLEN=-64;STRANDS=+-;STRANDS2=9,3,9,3;RE=12;REF_strand=226737,169675;Strandbias_pval=0.255222;AF=3.02715e-05 GT:DR:DV 0/0:396400:12 +chr20 4685874 21 AATATCACCACCTAAATCATCTCTTGCCTAAAACAAGGAGTAGAAAGTGAATGAAGGAAGGAACAGGTGATGGTCAGTGTCCTTTCTACGCCTCAAAATTTAAGAGTTTATGTGAAAATTCATAAATATTAATC N . PASS IMPRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4686001;STD_quant_start=23.668545;STD_quant_stop=30.796104;Kurtosis_quant_start=-0.675857;Kurtosis_quant_stop=-0.848016;SVTYPE=DEL;SUPTYPE=AL,NR;SVLEN=-127;STRANDS=+-;STRANDS2=9,1,9,1;RE=10;REF_strand=226504,169901;Strandbias_pval=0.0512664;AF=2.52267e-05 GT:DR:DV 0/0:396395:10 +chr20 4685915 22 GAATGAAGGAAGGAACA N . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4685932;STD_quant_start=3.276305;STD_quant_stop=4.946550;Kurtosis_quant_start=-1.326831;Kurtosis_quant_stop=-1.564823;SVTYPE=DEL;SUPTYPE=AL,NR;SVLEN=-17;STRANDS=+-;STRANDS2=102,56,102,56;RE=158;REF_strand=226726,169832;Strandbias_pval=0.0644297;AF=0.000398428 GT:DR:DV 0/0:396400:158 +chr20 4685896 23 N AAAAAAAAAAAAAAAAA . PASS IMPRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4685925;STD_quant_start=13.639146;STD_quant_stop=16.586297;Kurtosis_quant_start=-1.921070;Kurtosis_quant_stop=-2.172601;SVTYPE=INS;SUPTYPE=AL;SVLEN=11;STRANDS=+-;STRANDS2=47,30,47,30;RE=77;REF_strand=226732,169773;Strandbias_pval=0.565075;AF=0.000194197 GT:DR:DV 0/0:396428:77 +chr20 4685930 24 AGGTGATGGTCAGTGTCCTTTCTACGCCTCAAAATTTAAGAGTTTATGTGAAAATT N . PASS IMPRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4685985;STD_quant_start=6.844958;STD_quant_stop=12.887778;Kurtosis_quant_start=-1.648911;Kurtosis_quant_stop=-2.040576;SVTYPE=DEL;SUPTYPE=AL;SVLEN=-55;STRANDS=+-;STRANDS2=138,95,138,95;RE=233;REF_strand=226568,169976;Strandbias_pval=0.551461;AF=0.000587577 GT:DR:DV 0/0:396311:233 +chr20 4685985 25 ATTCATAAATAT N . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4685996;STD_quant_start=2.469818;STD_quant_stop=2.408319;Kurtosis_quant_start=0.428018;Kurtosis_quant_stop=0.115949;SVTYPE=DEL;SUPTYPE=AL,NR;SVLEN=-11;STRANDS=+-;STRANDS2=6,8,6,8;RE=14;REF_strand=226378,170124;Strandbias_pval=0.294268;AF=3.53088e-05 GT:DR:DV 0/0:396488:14 +chr20 4686021 26 N TTTTTTTTTTTT . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4686022;STD_quant_start=5.371220;STD_quant_stop=4.260282;Kurtosis_quant_start=-1.387474;Kurtosis_quant_stop=-1.021416;SVTYPE=INS;SUPTYPE=AL;SVLEN=11;STRANDS=+-;STRANDS2=25,15,25,15;RE=40;REF_strand=226037,170245;Strandbias_pval=0.52637;AF=0.000100938 GT:DR:DV 0/0:396242:40 +chr20 4686065 27 N AAAAAAAAAAAAAAAAA . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4686071;STD_quant_start=6.224950;STD_quant_stop=7.416198;Kurtosis_quant_start=-1.413762;Kurtosis_quant_stop=-1.837306;SVTYPE=INS;SUPTYPE=AL;SVLEN=12;STRANDS=+-;STRANDS2=15,9,15,9;RE=24;REF_strand=225615,170448;Strandbias_pval=0.68241;AF=6.05964e-05 GT:DR:DV 0/0:396039:24 +chr20 4686088 28 CCTTTCATTTT N . STRANDBIAS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4686099;STD_quant_start=3.305008;STD_quant_stop=1.664101;Kurtosis_quant_start=0.056747;Kurtosis_quant_stop=5.162091;SVTYPE=DEL;SUPTYPE=AL;SVLEN=-11;STRANDS=+-;STRANDS2=80,24,80,24;RE=104;REF_strand=225335,170554;Strandbias_pval=2.58828e-05;AF=0.0002627 GT:DR:DV 0/0:395785:104 +chr20 4686159 29 TGATTTTTACAG N . STRANDBIAS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4686183;STD_quant_start=3.400368;STD_quant_stop=5.755432;Kurtosis_quant_start=-0.312650;Kurtosis_quant_stop=-1.000987;SVTYPE=DEL;SUPTYPE=AL,NR;SVLEN=-24;STRANDS=+-;STRANDS2=7,25,7,25;RE=32;REF_strand=224491,170902;Strandbias_pval=9.62717e-05;AF=8.09321e-05 GT:DR:DV 0/0:395361:32 +chr20 4686196 30 GGCACCCGCAGGC N . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4686209;STD_quant_start=5.957857;STD_quant_stop=6.620179;Kurtosis_quant_start=-1.882003;Kurtosis_quant_stop=-0.555657;SVTYPE=DEL;SUPTYPE=AL,NR;SVLEN=-13;STRANDS=+-;STRANDS2=157,97,157,97;RE=254;REF_strand=224102,171052;Strandbias_pval=0.113133;AF=0.000642787 GT:DR:DV 0/0:394900:254 +chr20 4686249 31 N TTTTTTTTTTTTTTTTTTTT . STRANDBIAS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4686254;STD_quant_start=1.383128;STD_quant_stop=4.969472;Kurtosis_quant_start=-1.166223;Kurtosis_quant_stop=-1.432486;SVTYPE=INS;SUPTYPE=AL;SVLEN=12;STRANDS=+-;STRANDS2=36,10,36,10;RE=46;REF_strand=223389,171250;Strandbias_pval=0.00271375;AF=0.000116562 GT:DR:DV 0/0:394593:46 +chr20 4686272 32 GCGCTGCACCCTTTAACTTAAACCTCGGCCGGCCGCCCGCCGGGGGCACAGAGTGTGCGCCGGGCC N . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4686351;STD_quant_start=6.292853;STD_quant_stop=2.810694;Kurtosis_quant_start=-0.819339;Kurtosis_quant_stop=-1.018933;SVTYPE=DEL;SUPTYPE=AL;SVLEN=-79;STRANDS=+-;STRANDS2=8,13,8,13;RE=21;REF_strand=222364,171492;Strandbias_pval=0.121883;AF=5.3319e-05 GT:DR:DV 0/0:393835:21 +chr20 4686287 33 GCCGCCCGCCGGGGGCACAGAGTGTGCGCCGGGCCGCGCGGCAATTGGTCCCCGCGCCGACCTCCGCCCGCGAGCGCCGCCGCTTCCCTTCCCCGCCCCGCGTCCCT N . PASS IMPRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4686423;STD_quant_start=18.635987;STD_quant_stop=10.714476;Kurtosis_quant_start=-2.068375;Kurtosis_quant_stop=-1.911747;SVTYPE=DEL;SUPTYPE=AL,NR;SVLEN=-136;STRANDS=+-;STRANDS2=7,11,7,11;RE=18;REF_strand=221659,171658;Strandbias_pval=0.157072;AF=4.57646e-05 GT:DR:DV 0/0:393299:18 +chr20 4686302 34 N GAAGAAGAAGAAGC . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4686307;STD_quant_start=7.489993;STD_quant_stop=3.193744;Kurtosis_quant_start=-1.666775;Kurtosis_quant_stop=-1.234648;SVTYPE=INS;SUPTYPE=AL;SVLEN=14;STRANDS=+-;STRANDS2=14,6,14,6;RE=20;REF_strand=222401,171441;Strandbias_pval=0.264287;AF=5.07818e-05 GT:DR:DV 0/0:393822:20 +chr20 4686326 35 GGGGGCACAGAGTGTGCGCCGGGCCGCGCGGCAATTGGTCCCCGCGCCGACCTCCGCCCGCGAGCGCCGCCGCTTCCCTTCCCCGCCCCGCGTCCCTCCCCCTCGGCCCCGCGCGTCGCCTGTCCTCCGAGCCAGTCGCTGACAGCCGCGGCGCCGCGAGCTTCTCCTCTCCTCACGACCGAGGCAGGTAAACGCCCGGGGTGGGAGGAACGCGGGCGGGGGCAGGGGAGCCGCGGGGGCCGAGTGAGGACCCCGGGCCTCGGGTCCCAGGCGCAAGGGTGCCCGGCCGGGCGGGGTCGGGACCCCAGTGAGGAGGGGCCGGGGGCTGCCCCGCGGGCGCGTGACGCGTCTCGGGCCTGCCCGGCTGCGCTGGTCTCCGCTCGGGTGAGGCGGCTTGGCTTCGCTTTTCAGGTTAGGAAAGCTCCCTTTACTGCGCGTTGGGGGGCTGGGGGAGCTGGCGGAGCCCCGTTAGGGAGGTCGGTGGCGCCGGGGTGTCTCAGCGCCCCCTGCACCCCGCGCGGGTCCGGCCCAGCGGGCGATCGCTGGCGCCCAGGGAACTCCGGGAGGGCCGCCAGCGGGCTCCGCAGGGCGCGGGGCGGGGAGGGGCGCCTGGGGGCCGCGGGGCTCGCGCTCCCCGCCCGTTGGCCGCCCCTCGGAGGCCGAGATCGGGGCCCAGAACGCCCCTTGGCAAGGCCTGGCGCTTCCGCGATGCCCAGAGGGTGCTTGGGGGGATGGAGAGAGGGGCGCCCGCCG N . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4687079;STD_quant_start=0.301511;STD_quant_stop=0.452267;Kurtosis_quant_start=-0.931244;Kurtosis_quant_stop=1.071752;SVTYPE=DEL;SUPTYPE=AL;SVLEN=-753;STRANDS=+-;STRANDS2=50,38,50,38;RE=88;REF_strand=218355,173767;Strandbias_pval=0.914628;AF=0.00022442 GT:DR:DV 0/0:392034:88 +chr20 4686340 36 N GGTGGCGCAGCGC . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4686346;STD_quant_start=7.452413;STD_quant_stop=6.872465;Kurtosis_quant_start=-2.087832;Kurtosis_quant_stop=-1.576076;SVTYPE=INS;SUPTYPE=AL;SVLEN=11;STRANDS=+-;STRANDS2=12,15,12,15;RE=27;REF_strand=221897,171635;Strandbias_pval=0.24577;AF=6.86094e-05 GT:DR:DV 0/0:393505:27 +chr20 4686411 37 CCCCGCGTCCCT N . STRANDBIAS IMPRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4686437;STD_quant_start=8.169841;STD_quant_stop=10.322032;Kurtosis_quant_start=-1.809436;Kurtosis_quant_stop=-1.963281;SVTYPE=DEL;SUPTYPE=AL,NR;SVLEN=-26;STRANDS=+-;STRANDS2=344,469,344,469;RE=813;REF_strand=220593,171946;Strandbias_pval=2.69182e-15;AF=0.00207113 GT:DR:DV 0/0:391726:813 +chr20 4686485 38 CTTCTCCTCTCCTCA N . STRANDBIAS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4686501;STD_quant_start=4.120859;STD_quant_stop=4.963447;Kurtosis_quant_start=-1.252830;Kurtosis_quant_stop=-1.176444;SVTYPE=DEL;SUPTYPE=AL,NR;SVLEN=-16;STRANDS=+-;STRANDS2=259,66,259,66;RE=325;REF_strand=219732,172271;Strandbias_pval=5.28546e-19;AF=0.000829075 GT:DR:DV 0/0:391678:325 +chr20 4686508 39 N CGAAGCCCAACAGTG . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4686510;STD_quant_start=6.485025;STD_quant_stop=6.284903;Kurtosis_quant_start=-1.582240;Kurtosis_quant_stop=-1.622304;SVTYPE=INS;SUPTYPE=AL;SVLEN=11;STRANDS=+-;STRANDS2=21,15,21,15;RE=36;REF_strand=219546,172352;Strandbias_pval=0.867336;AF=9.18606e-05 GT:DR:DV 0/0:391862:36 +chr20 4686486 40 CTTCTCCTCTC N . STRANDBIAS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4686497;STD_quant_start=0.611418;STD_quant_stop=1.106480;Kurtosis_quant_start=-1.160993;Kurtosis_quant_stop=7.447596;SVTYPE=DEL;SUPTYPE=AL,NR;SVLEN=-11;STRANDS=+-;STRANDS2=85,131,83,133;RE=214;REF_strand=219757,172253;Strandbias_pval=9.2632e-07;AF=0.000545904 GT:DR:DV 0/0:391796:214 +chr20 4686492 41 CTCTCCTCACGACCGAGGCAGGTAAACGCCCGGGGTGGGAGGAACGCGGGCGGGGGCAGGGGAGCCGCGGGGGCCGAGTGAGGACCCCGGGCCTCGGGTCCCAGGCGCAAGGGTGCCCGGCCGGGCGGGGTCGGGACCCCA N . PASS IMPRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4686620;STD_quant_start=16.164777;STD_quant_stop=25.678785;Kurtosis_quant_start=-0.658661;Kurtosis_quant_stop=-1.533668;SVTYPE=DEL;SUPTYPE=AL,NR;SVLEN=-128;STRANDS=+-;STRANDS2=6,5,6,5;RE=11;REF_strand=219123,172667;Strandbias_pval=1;AF=2.80763e-05 GT:DR:DV 0/0:391779:11 +chr20 4686491 42 TCCTCTCCTCACGACCGAGGCAGGTAAACGCCCGGGGTGGGAGGAACGCGGGCGGGGGCAGGGGAGCCGCGGGGGCCGAGTGAGGACCCCGGGCCTCGGGTCCCAGGCGCAAGGGTGCCCGGCCGGGCGGGGTCGGGACCCCAGTGAGGAGGGGCCGGGGGCTGCCCCGCGGGCGCGTGACGCGTCTCGGGCCTGCCCGGCTGCGCTGGTCTCCGCTCGGGTGAGGCGGCTTGGCTTCGCTTTTCAGGTTAGGAAAGCTCCCTTTACTGCGCGTTGGGGGGCTGGGGGAGCTGGCGGAGCCCCGTTAGGGAGGTCGGTGGCGCCGGGGTGTCTCAGCGCCCCCTGCACCCCGCGCGGGTCCGGCCCAGCG N . PASS IMPRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4686860;STD_quant_start=20.916501;STD_quant_stop=21.968159;Kurtosis_quant_start=0.383174;Kurtosis_quant_stop=-1.083247;SVTYPE=DEL;SUPTYPE=AL;SVLEN=-369;STRANDS=+-;STRANDS2=8,3,8,3;RE=11;REF_strand=218075,173401;Strandbias_pval=0.365996;AF=2.80988e-05 GT:DR:DV 0/0:391465:11 +chr20 4686538 43 GCGGGCGGGGGCAGGGGAGCCGCGGGGGCCGAGTGAGGACCCCGGGCCTCGGGTCCCAGGCGCAAGGGTGCCCGGCCGGGCGGGGTCGGGACCCCAGTGAGGAGGGGCCGGGGGCTGCCCCGCGGGCGCGTGACGCGTCTCGGGCCTGCCCGGCTGCGCTGGTCTCCGCTCGGGTGAGGCGGCTTGGCTTCGCTTTTCAGGTTAGGAAAGCTCCCTTTACTGCGCGTTGGGGGGCTGGGGGAGCTGGCGGAGCCCCGTTAGGGAGGTCGGTGGCGCCGGGGTGTCTCAGCGCCCCCTGCACCCCGCGCGGGTCCGGCCCAGCGGGCGATCGCTGGCGCCCAGGGAACTCCGGGAGGGCCGCCAGCGGGCTCCGCAGGGCGCGGGGCGGGGAGGGGCGCCTGGGGGCCGCGGGGCTCGCGCTCCCCGCCCGTTGGCCGCCCCTCGGAGGCCGAGATCGGGGCCCAGAACGCCCCTTGGCAAGGCCTGGCGCTTCCGCGATGCCCAGAGGGTGCTTGGGGGGATGGAGAGAGGGGCGCCCGCCGGGGGAGTTCCGGGAGCCTCGGTGCCTCCCGCCGCAGCTGCAGCGTTCCTCCCGGGAGGCGGCCCAGCCCTTCATCCTCGCCGCCTGAGCTTCTCCGAGGGGGGCTGCAGCCTTGCGGCCGTTGCCACCGCCTGGAGAAGCGGCCCACGCGGACTGA N . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4687235;STD_quant_start=0.000000;STD_quant_stop=0.000000;Kurtosis_quant_start=3.230303;Kurtosis_quant_stop=1.621170;SVTYPE=DEL;SUPTYPE=AL;SVLEN=-697;STRANDS=+-;STRANDS2=34,19,34,19;RE=53;REF_strand=216486,174449;Strandbias_pval=0.215729;AF=0.000135572 GT:DR:DV 0/0:390882:53 +chr20 4686539 44 CGGGCGGGGGCA N . STRANDBIAS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4686550;STD_quant_start=3.843125;STD_quant_stop=2.930569;Kurtosis_quant_start=-1.341098;Kurtosis_quant_stop=-0.771900;SVTYPE=DEL;SUPTYPE=AL,NR;SVLEN=-11;STRANDS=+-;STRANDS2=150,259,150,259;RE=409;REF_strand=219041,172509;Strandbias_pval=5.58291e-15;AF=0.00104457 GT:DR:DV 0/0:391141:409 +chr20 4686560 45 GGGGGCCGAGTGAGGACCCCGGGCCTCGGGTCCCAGGCGCAAGGGTGCCCGGCCGGGCGGGGTCGGGACCCCAGTGAGGAGGGGCCGGGGGCTGCCCCGCGGGCGCGTGACGCGTCTCGGGCCTGCCCGGCTGCGCTGGTCTCCGCTCGGGTGAGGCGGCTTGGCTTCGCTTTTCAGGTTAGGAAAGCTCCCTTTACTGCGCGTTGGGGGGCTGGGGGAGCTGGCGGAGCCCCGTTAGGGAGGTCGGTGGCGCCGGGGTGTCTCAGCGCCCCCTGCACCCCGCGCGGGTCCGGCCCAGCGGGCGATCGCTGGCGCCCAGGGAACTCCGGGAGGGCCGCCAGCGGGCTCCGCAGGGCGCGGGGCGGGGAGGGGCGCCT N . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4686938;STD_quant_start=4.494441;STD_quant_stop=4.878524;Kurtosis_quant_start=-0.951142;Kurtosis_quant_stop=0.802392;SVTYPE=DEL;SUPTYPE=AL;SVLEN=-378;STRANDS=+-;STRANDS2=7,9,7,9;RE=16;REF_strand=217297,173802;Strandbias_pval=0.451755;AF=4.09104e-05 GT:DR:DV 0/0:391083:16 +chr20 4686568 46 AGTGAGGACCCCGGGCCTCGGGTCCCAGGCGCAAGGGTGCCCGGCCGGGCGGGGTCGGGACCCCAGTGAGGAGGGGCCGGGGGCTGCCCCGCGGGCGCGTGACGCGT N . PASS IMPRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4686675;STD_quant_start=14.855975;STD_quant_stop=8.396428;Kurtosis_quant_start=-1.744371;Kurtosis_quant_stop=-0.889422;SVTYPE=DEL;SUPTYPE=AL;SVLEN=-107;STRANDS=+-;STRANDS2=7,9,7,9;RE=16;REF_strand=218475,173080;Strandbias_pval=0.451306;AF=4.08627e-05 GT:DR:DV 0/0:391539:16 +chr20 4686543 47 GGGGGCAGGGGAGCCGCGGGGGCCGAGTGAGGACCCCGGGCCTCGGGTCCCAGGCGCAAGGGTGCCCGGCCGGGCGGGGTCGGGACCCCAGTGAGGAGGGGCCGGGGGCTGCCCCGCGGGCGCGTGACGCGTCTCGGGCCTGCCCGGCTGCGCTGGTCTCCGCTCGGGTGAGGCGGCTTGGCTTCGCTTTTCAGGTTAGGAAAGCTCCCTTTACTGCGCGTTGGGGGGCTGGGGGAGCTGGCGGAGCCCCGTTAGGGAGGTCGGTGGCGCCGGGGTGTCTCAGCGCCCCCTGCACCCCGCGCGGGTCCGGCCCAGCGGGCGATCGCTGGCGCCCAGGGAACTCCGGGAGGGCCGCCAGCGGGCTCCGCAGGGCGCGGGGCGGGGAGGGGCGCCTGGGGGCCGCGGGGCTCGCGCTCCCCGCCCGTTGGCCGCCCCTCGGAGGCCGAGATCGGGGCCCAGAACGCCCCTTGGCAAGGCCTGGCGCTTCCGCGATGCCCAGAGGGTGCTTGGGGGGATGGAGAGAGGGGCGCCCGCCGGGGGAGTTCCGGGAGCCTCGGTGCCTCCCGCCGCAGCTGCAGCGTTCCTCCCGGGAGGCGGCCCAGCCCTTCATCCTCGCCGCCTGAGCTTCTCCGAGGGGGGCTGCAGCCTTGCGGCCGTTGCCACCGCCTGGAGAAGCGGCCCACGCGGACTGACGGGCG N . STRANDBIAS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4687241;STD_quant_start=3.316625;STD_quant_stop=3.273268;Kurtosis_quant_start=0.619020;Kurtosis_quant_stop=-1.814115;SVTYPE=DEL;SUPTYPE=AL;SVLEN=-698;STRANDS=+-;STRANDS2=15,28,15,28;RE=43;REF_strand=216433,174462;Strandbias_pval=0.00853518;AF=0.000110004 GT:DR:DV 0/0:390852:43 +chr20 4686560 48 N GGGGGAAGGAGAGGGA . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4686567;STD_quant_start=7.765307;STD_quant_stop=8.378544;Kurtosis_quant_start=-2.049368;Kurtosis_quant_stop=-1.141485;SVTYPE=INS;SUPTYPE=AL;SVLEN=12;STRANDS=+-;STRANDS2=14,5,14,5;RE=19;REF_strand=218878,172634;Strandbias_pval=0.164853;AF=4.85298e-05 GT:DR:DV 0/0:391493:19 +chr20 4686668 49 AGGGGCCGGGGGCTGCCCCGCGGGCGCGTGACGCGTCTCGGGCCTGCCCGGCTGCGCTGGTCTCCGCTCGGGTGAGGCGGCTTGGCTTCGCTTTTCAGGTTAGGAAAGCTCCCTT N . PASS IMPRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4686751;STD_quant_start=7.713624;STD_quant_stop=14.621901;Kurtosis_quant_start=-1.744925;Kurtosis_quant_stop=-1.889944;SVTYPE=DEL;SUPTYPE=AL,NR;SVLEN=-83;STRANDS=+-;STRANDS2=16,4,16,4;RE=20;REF_strand=217719,173610;Strandbias_pval=0.0402063;AF=5.11079e-05 GT:DR:DV 0/0:391309:20 +chr20 4686697 50 N GCGGCGCCGATCGGC . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4686701;STD_quant_start=6.070420;STD_quant_stop=5.064583;Kurtosis_quant_start=-1.826190;Kurtosis_quant_stop=-1.838215;SVTYPE=INS;SUPTYPE=AL;SVLEN=12;STRANDS=+-;STRANDS2=25,15,25,15;RE=40;REF_strand=217940,173559;Strandbias_pval=0.428788;AF=0.000102171 GT:DR:DV 0/0:391459:40 +chr20 4686725 51 TTGGCTTCGCTTTTCAGGTTAGGAAAGCTCCCTTTACTGCGCGTTGGGGGGCTGGGGGAGCTGGCGGAGCCCCGTTAGGGAGGTCGGTGGCGCCGGGGTGTCTCAGCGCCCCCTGCACCCCGCGCGGGTCCGGCCCA N . PASS IMPRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4686849;STD_quant_start=15.023315;STD_quant_stop=14.226735;Kurtosis_quant_start=-1.032157;Kurtosis_quant_stop=-1.305222;SVTYPE=DEL;SUPTYPE=AL;SVLEN=-124;STRANDS=+-;STRANDS2=3,10,3,10;RE=13;REF_strand=217048,174074;Strandbias_pval=0.0240357;AF=3.32377e-05 GT:DR:DV 0/0:391109:13 +chr20 4686749 52 N CCCCCCCCCCCCCCCCCC . PASS IMPRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4686758;STD_quant_start=10.009995;STD_quant_stop=9.418068;Kurtosis_quant_start=-1.869789;Kurtosis_quant_stop=-1.587727;SVTYPE=INS;SUPTYPE=AL;SVLEN=12;STRANDS=+-;STRANDS2=12,7,12,7;RE=19;REF_strand=217278,173856;Strandbias_pval=0.645879;AF=4.85767e-05 GT:DR:DV 0/0:391115:19 +chr20 4686785 53 GCCCCGTTAGGGAG N . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4686802;STD_quant_start=4.910061;STD_quant_stop=2.877952;Kurtosis_quant_start=-1.452542;Kurtosis_quant_stop=-1.087289;SVTYPE=DEL;SUPTYPE=AL,NR;SVLEN=-17;STRANDS=+-;STRANDS2=55,38,55,38;RE=93;REF_strand=216912,174105;Strandbias_pval=0.531692;AF=0.000237841 GT:DR:DV 0/0:390924:93 +chr20 4686815 54 GGGGTGTCTCAGCGCCCCCTGCACCCCGCGCGGGTCCGGCCCAGCGGGCGATCGCTGGCGCCCAGGGAACTCCGGGAGGGCCGCCAGCGGGCTCCGCAGGGCGCGGGGCGGGGAGGGGCGCCT N . PASS IMPRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4686937;STD_quant_start=12.907362;STD_quant_stop=16.757088;Kurtosis_quant_start=-0.211908;Kurtosis_quant_stop=-0.748951;SVTYPE=DEL;SUPTYPE=AL,NR;SVLEN=-122;STRANDS=+-;STRANDS2=7,5,7,5;RE=12;REF_strand=216218,174622;Strandbias_pval=1;AF=3.07031e-05 GT:DR:DV 0/0:390828:12 +chr20 4686809 55 N AGGGCGAGGCGGCGGCGAAGAAGGCTGCCGT . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4686826;STD_quant_start=9.290193;STD_quant_stop=5.030675;Kurtosis_quant_start=-2.063179;Kurtosis_quant_stop=-1.742861;SVTYPE=INS;SUPTYPE=AL;SVLEN=11;STRANDS=+-;STRANDS2=16,10,16,10;RE=26;REF_strand=216707,174246;Strandbias_pval=0.561149;AF=6.65042e-05 GT:DR:DV 0/0:390927:26 +chr20 4686805 56 GTGGCGCCGGGGTGTCTCAGCGCCCCCTGCACC N . PASS IMPRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4686842;STD_quant_start=11.923486;STD_quant_stop=10.448217;Kurtosis_quant_start=-1.750308;Kurtosis_quant_stop=-1.777573;SVTYPE=DEL;SUPTYPE=AL;SVLEN=-37;STRANDS=+-;STRANDS2=490,443,490,443;RE=933;REF_strand=216674,174306;Strandbias_pval=0.0804978;AF=0.00238631 GT:DR:DV 0/0:390047:933 +chr20 4686885 57 GGGCCGCCAGC N . STRANDBIAS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4686902;STD_quant_start=1.294961;STD_quant_stop=1.430438;Kurtosis_quant_start=5.184281;Kurtosis_quant_stop=3.732866;SVTYPE=DEL;SUPTYPE=AL;SVLEN=-17;STRANDS=+-;STRANDS2=37,94,37,94;RE=131;REF_strand=216010,174767;Strandbias_pval=5.21205e-10;AF=0.00033523 GT:DR:DV 0/0:390646:131 +chr20 4686928 58 TCCCCGCCCGTTGG N . STRANDBIAS IMPRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4686971;STD_quant_start=7.842249;STD_quant_stop=12.353489;Kurtosis_quant_start=-1.719762;Kurtosis_quant_stop=-1.792902;SVTYPE=DEL;SUPTYPE=AL,NR;SVLEN=-43;STRANDS=+-;STRANDS2=479,671,479,671;RE=1150;REF_strand=215595,175124;Strandbias_pval=4.77756e-20;AF=0.00294329 GT:DR:DV 0/0:389569:1150 +chr20 4686967 59 N TTGGCTTGGCC . STRANDBIAS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4686970;STD_quant_start=6.875517;STD_quant_stop=5.981031;Kurtosis_quant_start=-1.841236;Kurtosis_quant_stop=-1.865587;SVTYPE=INS;SUPTYPE=AL;SVLEN=11;STRANDS=+-;STRANDS2=36,9,36,9;RE=45;REF_strand=215461,175251;Strandbias_pval=0.000780863;AF=0.000115174 GT:DR:DV 0/0:390667:45 +chr20 4686997 60 CCCAGAACGCC N . STRANDBIAS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4687008;STD_quant_start=2.143441;STD_quant_stop=2.375186;Kurtosis_quant_start=-0.616709;Kurtosis_quant_stop=1.624505;SVTYPE=DEL;SUPTYPE=AL,NR;SVLEN=-11;STRANDS=+-;STRANDS2=149,64,149,64;RE=213;REF_strand=215189,175455;Strandbias_pval=1.23221e-05;AF=0.000545253 GT:DR:DV 0/0:390431:213 +chr20 4687033 61 CGCTTCCGCGATGCCCAGAGGGTGCTTGGGGGGATGGAGAGAGGGGCGCCCGCCGGGGGAGTTCCGGGAGCCTCGGTGCCTCCCGCCGCAGCTGCAGCGTTCCTCC N . PASS IMPRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4687130;STD_quant_start=17.515707;STD_quant_stop=9.741663;Kurtosis_quant_start=-1.198415;Kurtosis_quant_stop=0.386949;SVTYPE=DEL;SUPTYPE=AL,NR;SVLEN=-97;STRANDS=+-;STRANDS2=5,6,4,7;RE=10;REF_strand=214688,175980;Strandbias_pval=0.55834;AF=2.55972e-05 GT:DR:DV 0/0:390658:10 +chr20 4687051 62 N GGGGGGGGGGGGG . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4687052;STD_quant_start=3.588175;STD_quant_stop=4.962358;Kurtosis_quant_start=-1.343284;Kurtosis_quant_stop=-1.486974;SVTYPE=INS;SUPTYPE=AL;SVLEN=12;STRANDS=+-;STRANDS2=25,7,25,7;RE=32;REF_strand=214860,175823;Strandbias_pval=0.0116106;AF=8.19078e-05 GT:DR:DV 0/0:390651:32 +chr20 4687066 63 AGGGGCGCCCGCCGGGGGAGTTCC N . STRANDBIAS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4687087;STD_quant_start=7.499923;STD_quant_stop=7.628923;Kurtosis_quant_start=-1.375658;Kurtosis_quant_stop=-1.262954;SVTYPE=DEL;SUPTYPE=AL;SVLEN=-21;STRANDS=+-;STRANDS2=362,507,362,507;RE=869;REF_strand=214705,175983;Strandbias_pval=5.03165e-15;AF=0.00222428 GT:DR:DV 0/0:389819:869 +chr20 4687107 64 GCCCACGCGGACTGA N . PASS IMPRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4687203;STD_quant_start=16.682326;STD_quant_stop=11.631853;Kurtosis_quant_start=-0.705311;Kurtosis_quant_stop=-1.103982;SVTYPE=DEL;SUPTYPE=AL,NR;SVLEN=-96;STRANDS=+-;STRANDS2=7,4,7,4;RE=11;REF_strand=214306,176282;Strandbias_pval=0.76396;AF=2.81627e-05 GT:DR:DV 0/0:390577:11 +chr20 4687128 65 CCCGGGAGGCGG N . STRANDBIAS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4687140;STD_quant_start=4.118307;STD_quant_stop=4.415561;Kurtosis_quant_start=-0.470723;Kurtosis_quant_stop=-1.505664;SVTYPE=DEL;SUPTYPE=AL,NR;SVLEN=-12;STRANDS=+-;STRANDS2=244,110,244,110;RE=354;REF_strand=214379,176287;Strandbias_pval=7.68654e-08;AF=0.000906145 GT:DR:DV 0/0:390312:354 +chr20 4687112 66 N GCAGGCGGCACGCACAGCCAAGAATGGGAA . PASS IMPRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4687124;STD_quant_start=6.557439;STD_quant_stop=10.095003;Kurtosis_quant_start=-1.999996;Kurtosis_quant_stop=-2.052365;SVTYPE=INS;SUPTYPE=AL;SVLEN=11;STRANDS=+-;STRANDS2=12,11,12,11;RE=23;REF_strand=214491,176215;Strandbias_pval=0.83607;AF=5.88678e-05 GT:DR:DV 0/0:390683:23 +chr20 4687160 67 N TTCTCCTCCTCCTCCTCA . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4687168;STD_quant_start=5.297798;STD_quant_stop=7.307530;Kurtosis_quant_start=-1.839261;Kurtosis_quant_stop=-2.026138;SVTYPE=INS;SUPTYPE=AL;SVLEN=11;STRANDS=+-;STRANDS2=20,11,20,11;RE=31;REF_strand=214273,176409;Strandbias_pval=0.36718;AF=7.93484e-05 GT:DR:DV 0/0:390651:31 +chr20 4687223 68 CACGCGGACTGACGGGCGGGGGCGGGGCCTCGGGCCTCGGCGG N . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4687263;STD_quant_start=2.150581;STD_quant_stop=5.820223;Kurtosis_quant_start=-0.788231;Kurtosis_quant_stop=-1.736301;SVTYPE=DEL;SUPTYPE=AL;SVLEN=-40;STRANDS=+-;STRANDS2=17,16,17,16;RE=33;REF_strand=213815,176416;Strandbias_pval=0.729259;AF=8.45653e-05 GT:DR:DV 0/0:390198:33 +chr20 4687306 69 GGCGGGGAGAGAGGAGCTGCAGGTCTGCGGCCTGGCCC N . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4687334;STD_quant_start=7.334131;STD_quant_stop=9.808696;Kurtosis_quant_start=-1.306558;Kurtosis_quant_stop=-1.789353;SVTYPE=DEL;SUPTYPE=AL,NR;SVLEN=-28;STRANDS=+-;STRANDS2=23,16,23,16;RE=39;REF_strand=213290,176413;Strandbias_pval=0.632602;AF=0.000100076 GT:DR:DV 0/0:389664:39 +chr20 4687385 70 CCAGTCCCCCTGGAGGGAGAACGCTGGCCATGGGGGGCTCCAAGGAACAACCAGCCTCG N . STRANDBIAS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4687441;STD_quant_start=9.284396;STD_quant_stop=2.966479;Kurtosis_quant_start=-1.492914;Kurtosis_quant_stop=-0.413704;SVTYPE=DEL;SUPTYPE=AL,NR;SVLEN=-56;STRANDS=+-;STRANDS2=15,2,15,2;RE=17;REF_strand=212805,176412;Strandbias_pval=0.00581638;AF=4.36774e-05 GT:DR:DV 0/0:389200:17 +chr20 4687384 71 ATTCCTCCCAGTCCCCCTGGAGGGAGAACGCTGGCCATGGGGGGCTCCAAGGAACAACCAGCCTCGGATGACGACCCTTGGGTCACCGGTCTCCCCACCTGTGCGGCA N . STRANDBIAS IMPRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4687489;STD_quant_start=10.733126;STD_quant_stop=13.754999;Kurtosis_quant_start=0.290288;Kurtosis_quant_stop=-1.616308;SVTYPE=DEL;SUPTYPE=AL;SVLEN=-105;STRANDS=+-;STRANDS2=14,2,14,2;RE=16;REF_strand=212668,176410;Strandbias_pval=0.00989766;AF=4.11229e-05 GT:DR:DV 0/0:389062:16 +chr20 4687416 72 N GGGGGGGGGGGGGGGG . PASS IMPRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4687431;STD_quant_start=13.168776;STD_quant_stop=9.729680;Kurtosis_quant_start=-2.192060;Kurtosis_quant_stop=-1.988956;SVTYPE=INS;SUPTYPE=AL;SVLEN=13;STRANDS=+-;STRANDS2=14,11,14,11;RE=25;REF_strand=212733,176412;Strandbias_pval=1;AF=6.42434e-05 GT:DR:DV 0/0:389120:25 +chr20 4687497 73 ATTATTAAACAATGGGGAGAAATCCATGTTTACTGTCCTTTTTAAGGAATTTTTTGCTCTTCTCTTTGAGGTGGCTGTAGGAAATAGATTTTTT N . PASS IMPRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4687596;STD_quant_start=13.307892;STD_quant_stop=6.595453;Kurtosis_quant_start=-1.703839;Kurtosis_quant_stop=0.934814;SVTYPE=DEL;SUPTYPE=AL,NR;SVLEN=-99;STRANDS=+-;STRANDS2=9,3,9,3;RE=12;REF_strand=211991,176408;Strandbias_pval=0.245747;AF=3.08961e-05 GT:DR:DV 0/0:388387:12 +chr20 4687540 74 TTTTAAGGAATTTTTTGCTCTTCTC N . STRANDBIAS IMPRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4687566;STD_quant_start=12.662958;STD_quant_stop=14.881317;Kurtosis_quant_start=-1.873571;Kurtosis_quant_stop=-1.909538;SVTYPE=DEL;SUPTYPE=AL,NR;SVLEN=-26;STRANDS=+-;STRANDS2=252,137,252,137;RE=389;REF_strand=211949,176408;Strandbias_pval=5.40417e-05;AF=0.00100166 GT:DR:DV 0/0:387968:389 +chr20 4687590 75 N TTTTTTTTTTTTTTTTTTTTTTTTTTT . STRANDBIAS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4687593;STD_quant_start=0.000000;STD_quant_stop=1.761953;Kurtosis_quant_start=-0.322837;Kurtosis_quant_stop=-0.788075;SVTYPE=INS;SUPTYPE=AL;SVLEN=11;STRANDS=+-;STRANDS2=122,13,122,13;RE=135;REF_strand=211652,176408;Strandbias_pval=1.76587e-19;AF=0.000347884 GT:DR:DV 0/0:387925:135 +chr20 4687660 76 N ATTTTTTTTTTTT . STRANDBIAS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4687660;STD_quant_start=1.905670;STD_quant_stop=4.712805;Kurtosis_quant_start=-1.492197;Kurtosis_quant_stop=-1.402430;SVTYPE=INS;SUPTYPE=AL;SVLEN=12;STRANDS=+-;STRANDS2=29,9,29,9;RE=38;REF_strand=211236,176406;Strandbias_pval=0.00832228;AF=9.80286e-05 GT:DR:DV 0/0:387604:38 +chr20 4687785 77 N CACAATAAAGGGAAAATATATATATAG . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4687801;STD_quant_start=9.224966;STD_quant_stop=8.018728;Kurtosis_quant_start=-1.850450;Kurtosis_quant_stop=-1.057477;SVTYPE=INS;SUPTYPE=AL;SVLEN=11;STRANDS=+-;STRANDS2=7,8,7,8;RE=15;REF_strand=210490,176397;Strandbias_pval=0.609867;AF=3.8771e-05 GT:DR:DV 0/0:386872:15 +chr20 4687777 78 TAGCAGTTCCCCATATGATTTGAAGTGTTTCCCGTTTCCTTAGGGAAAACTCCTGGTAGAATAGGATTAAGGATTTTTACAAATATAATTATCAAAAACATAGGAACAGGG N . PASS IMPRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4687867;STD_quant_start=13.512957;STD_quant_stop=13.935566;Kurtosis_quant_start=-0.090757;Kurtosis_quant_stop=0.587174;SVTYPE=DEL;SUPTYPE=AL;SVLEN=-90;STRANDS=+-;STRANDS2=7,3,7,3;RE=10;REF_strand=210331,176393;Strandbias_pval=0.362506;AF=2.58582e-05 GT:DR:DV 0/0:386714:10 +chr20 4687847 79 N TTTTTTTTTTT . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4687847;STD_quant_start=3.227486;STD_quant_stop=3.651484;Kurtosis_quant_start=-1.254439;Kurtosis_quant_stop=-1.808687;SVTYPE=INS;SUPTYPE=AL;SVLEN=11;STRANDS=+-;STRANDS2=16,9,16,9;RE=25;REF_strand=210186,176392;Strandbias_pval=0.42311;AF=6.467e-05 GT:DR:DV 0/0:386553:25 +chr20 4687867 80 N AAAAAATGCAATGTAC . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4687873;STD_quant_start=0.277350;STD_quant_stop=4.009604;Kurtosis_quant_start=-0.049142;Kurtosis_quant_stop=-1.193761;SVTYPE=INS;SUPTYPE=AL;SVLEN=11;STRANDS=+-;STRANDS2=17,9,17,9;RE=26;REF_strand=210061,176388;Strandbias_pval=0.326008;AF=6.72793e-05 GT:DR:DV 0/0:386423:26 +chr20 4687972 81 N . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4688005;STD_quant_start=7.214569;STD_quant_stop=6.447868;Kurtosis_quant_start=-1.668283;Kurtosis_quant_stop=-1.991686;SVTYPE=DEL;SUPTYPE=AL;SVLEN=-33;STRANDS=+-;STRANDS2=91,69,91,69;RE=160;REF_strand=208942,176238;Strandbias_pval=0.5262;AF=0.00041539 GT:DR:DV 0/0:385020:160 +chr20 4688011 82 N AAAAAAAAAAAA . STRANDBIAS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4688011;STD_quant_start=0.000000;STD_quant_stop=2.976095;Kurtosis_quant_start=1.030463;Kurtosis_quant_stop=-0.993490;SVTYPE=INS;SUPTYPE=AL;SVLEN=12;STRANDS=+-;STRANDS2=8,34,8,34;RE=42;REF_strand=208266,175944;Strandbias_pval=6.08019e-06;AF=0.000109315 GT:DR:DV 0/0:384168:42 +chr20 28640917 83 N TCCCTTTCTTTCTTTCTTTCTTTCTTT . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=28640922;STD_quant_start=0.000000;STD_quant_stop=4.314555;Kurtosis_quant_start=-1.057415;Kurtosis_quant_stop=-1.382190;SVTYPE=INS;SUPTYPE=AL;SVLEN=27;STRANDS=+-;STRANDS2=3,23,3,23;RE=26;REF_strand=54,96;Strandbias_pval=0.0128723;AF=0.173333 GT:DR:DV 0/0:124:26 +chr20 28641002 84 N CTCCCCTTTCCTAACCTTCCTTGCTCTCTTCCTTCTTTCCTTCCCCTTCCCTTCTTTCCTTCCTTCCCCCTTCCTTTCCTTTCCTTTCCTTTCCTTTCCTTTCCT . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=28641004;STD_quant_start=4.764452;STD_quant_stop=6.978539;Kurtosis_quant_start=0.735697;Kurtosis_quant_stop=0.810797;SVTYPE=INS;SUPTYPE=AL;SVLEN=72;STRANDS=+-;STRANDS2=5,7,5,7;RE=12;REF_strand=54,96;Strandbias_pval=0.759172;AF=0.08 GT:DR:DV 0/0:138:12 +chr20 28640993 85 N TAACCTTCCCTTGCTCTCCTTCCCTCT . PASS IMPRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=28641013;STD_quant_start=4.857983;STD_quant_stop=16.153431;Kurtosis_quant_start=1.506831;Kurtosis_quant_stop=-2.184217;SVTYPE=INS;SUPTYPE=AL;SVLEN=18;STRANDS=+-;STRANDS2=14,16,14,16;RE=30;REF_strand=54,96;Strandbias_pval=0.305378;AF=0.2 GT:DR:DV 0/0:120:30 +chr20 28641119 86 N CCTTCCTTCCT . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=28641119;STD_quant_start=1.911066;STD_quant_stop=1.967121;Kurtosis_quant_start=-1.761895;Kurtosis_quant_stop=-1.152495;SVTYPE=INS;SUPTYPE=AL;SVLEN=11;STRANDS=+-;STRANDS2=20,27,20,27;RE=47;REF_strand=52,96;Strandbias_pval=0.388417;AF=0.317568 GT:DR:DV 0/1:101:47 +chr20 29408712 87 N TCTCTCCTTCCGTTTCTA . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=29408712;STD_quant_start=0.632456;STD_quant_stop=0.547723;Kurtosis_quant_start=-0.047472;Kurtosis_quant_stop=1.545097;SVTYPE=INS;SUPTYPE=AL;SVLEN=18;STRANDS=+-;STRANDS2=7,12,7,12;RE=19;REF_strand=18,26;Strandbias_pval=1;AF=0.431818 GT:DR:DV 0/1:25:19 diff --git a/SVs_sniffles/vcf/57265_bodySnif.vcf b/SVs_sniffles/vcf/57265_bodySnif.vcf new file mode 100644 index 0000000..4869852 --- /dev/null +++ b/SVs_sniffles/vcf/57265_bodySnif.vcf @@ -0,0 +1,39 @@ +##fileformat=VCFv4.1 +##source=Sniffles +##fileDate=20210810:57:55 AMef_minus +##contig= +##ALT= +##ALT= +##ALT= +##ALT= +##ALT= +##ALT= +##FILTER= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##FORMAT= +##FORMAT= +##FORMAT= +#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT bamfilt/57265_f.bam +chr20 4699380 0 N GGTGGTGGCTGGGGGCAGCCTTCATGGTGGTGGCTGGGGGCAGCCTCATGGTGGTGGCTGGGGGCAGCCTCATGGTGGTGGCTGGGGCAGCCTCAT . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4699381;STD_quant_start=0.000000;STD_quant_stop=1.891324;Kurtosis_quant_start=2.052346;Kurtosis_quant_stop=1.985101;SVTYPE=INS;SUPTYPE=AL;SVLEN=95;STRANDS=+-;STRANDS2=1050,1064,1050,1064;RE=2114;REF_strand=9910,10756;Strandbias_pval=0.137448;AF=0.102294 GT:DR:DV 0/0:18552:2114 +chr20 4699439 1 N GGGGGCAGCCTCATGGTGGTGGCTGGGGTACCATGGTGGTGGCTGGGGGCAGCCTCATGGTGGTGGCTGGGGGGCAGCCTCATGGTGGTGGGCT . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4699439;STD_quant_start=8.468973;STD_quant_stop=8.726298;Kurtosis_quant_start=-1.811511;Kurtosis_quant_stop=-1.865902;SVTYPE=INS;SUPTYPE=AL;SVLEN=95;STRANDS=+-;STRANDS2=1359,1434,1359,1434;RE=2793;REF_strand=9910,10756;Strandbias_pval=0.492747;AF=0.13515 GT:DR:DV 0/0:17873:2793 +chr20 4699493 2 N GCCTCCTCACGGTGGTGGCTGGGGGCAGCCTCATGGTGGTGGCTGGGGGCAGCTGTGGTGGTGGCTTCCAGGGACAGCCTCATGGTGAATGGCTGGGAC . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4699500;STD_quant_start=0.652863;STD_quant_stop=3.973271;Kurtosis_quant_start=4.509145;Kurtosis_quant_stop=-1.138564;SVTYPE=INS;SUPTYPE=AL;SVLEN=87;STRANDS=+-;STRANDS2=59,63,59,63;RE=122;REF_strand=9910,10756;Strandbias_pval=0.927917;AF=0.00590342 GT:DR:DV 0/0:20544:122 diff --git a/SVs_sniffles/vcf/57265_promoterSnif.vcf b/SVs_sniffles/vcf/57265_promoterSnif.vcf new file mode 100644 index 0000000..6a3d2aa --- /dev/null +++ b/SVs_sniffles/vcf/57265_promoterSnif.vcf @@ -0,0 +1,36 @@ +##fileformat=VCFv4.1 +##source=Sniffles +##fileDate=20210811:53:05 AMef_minus +##contig= +##ALT= +##ALT= +##ALT= +##ALT= +##ALT= +##ALT= +##FILTER= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##FORMAT= +##FORMAT= +##FORMAT= +#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT promoterbamfilt/57265_f.bam diff --git a/SVs_sniffles/vcf/57749_bodySnif.vcf b/SVs_sniffles/vcf/57749_bodySnif.vcf new file mode 100644 index 0000000..e3b8a70 --- /dev/null +++ b/SVs_sniffles/vcf/57749_bodySnif.vcf @@ -0,0 +1,38 @@ +##fileformat=VCFv4.1 +##source=Sniffles +##fileDate=20210810:58:50 AMef_minus +##contig= +##ALT= +##ALT= +##ALT= +##ALT= +##ALT= +##ALT= +##FILTER= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##FORMAT= +##FORMAT= +##FORMAT= +#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT bamfilt/57749_f.bam +chr20 4699380 0 N GGTGGTGGCTGGGGGCAGCCTCATGGTGGTGGCTGGGGGCAGCCTCAT . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4699380;STD_quant_start=0.990464;STD_quant_stop=2.554328;Kurtosis_quant_start=-1.274682;Kurtosis_quant_stop=-1.252426;SVTYPE=INS;SUPTYPE=AL;SVLEN=48;STRANDS=+-;STRANDS2=1193,1125,1193,1125;RE=2318;REF_strand=6670,6684;Strandbias_pval=0.177094;AF=0.173581 GT:DR:DV 0/0:11036:2318 +chr20 4699439 1 N GGGGCAGCCTCATGGTGGTGGCTGGGGGCAGCCTCATGGTGGTGGCT . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4699439;STD_quant_start=3.032372;STD_quant_stop=3.070348;Kurtosis_quant_start=-1.014873;Kurtosis_quant_stop=-0.780979;SVTYPE=INS;SUPTYPE=AL;SVLEN=47;STRANDS=+-;STRANDS2=459,473,459,473;RE=932;REF_strand=6670,6684;Strandbias_pval=0.684469;AF=0.0697918 GT:DR:DV 0/0:12422:932 diff --git a/SVs_sniffles/vcf/57749_promoterSnif.vcf b/SVs_sniffles/vcf/57749_promoterSnif.vcf new file mode 100644 index 0000000..dd2efbc --- /dev/null +++ b/SVs_sniffles/vcf/57749_promoterSnif.vcf @@ -0,0 +1,107 @@ +##fileformat=VCFv4.1 +##source=Sniffles +##fileDate=20210811:53:05 AMef_minus +##contig= +##ALT= +##ALT= +##ALT= +##ALT= +##ALT= +##ALT= +##FILTER= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##FORMAT= +##FORMAT= +##FORMAT= +#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT promoterbamfilt/57749_f.bam +chr20 4685109 0 CTCCTGGCTTCTC N . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4685122;STD_quant_start=6.059231;STD_quant_stop=7.057586;Kurtosis_quant_start=-1.537499;Kurtosis_quant_stop=-1.761368;SVTYPE=DEL;SUPTYPE=AL;SVLEN=-13;STRANDS=+-;STRANDS2=29,13,29,13;RE=42;REF_strand=104721,80932;Strandbias_pval=0.119346;AF=0.000226229 GT:DR:DV 0/0:185611:42 +chr20 4685141 1 CTCCCCTGCAACT N . STRANDBIAS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4685158;STD_quant_start=6.244998;STD_quant_stop=5.669467;Kurtosis_quant_start=-1.871864;Kurtosis_quant_stop=-1.707446;SVTYPE=DEL;SUPTYPE=AL;SVLEN=-17;STRANDS=+-;STRANDS2=12,31,12,31;RE=43;REF_strand=104761,81144;Strandbias_pval=0.000286827;AF=0.000231301 GT:DR:DV 0/0:185862:43 +chr20 4685224 2 AGCTTTTTTTTTTT N . STRANDBIAS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4685235;STD_quant_start=1.270001;STD_quant_stop=2.002686;Kurtosis_quant_start=-1.158471;Kurtosis_quant_stop=-0.811201;SVTYPE=DEL;SUPTYPE=AL,NR;SVLEN=-11;STRANDS=+-;STRANDS2=150,36,150,36;RE=186;REF_strand=104807,81503;Strandbias_pval=3.55884e-12;AF=0.000998336 GT:DR:DV 0/0:186124:186 +chr20 4685224 3 N TTTTTTTTTTTTTTTTTTTTTT . STRANDBIAS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4685224;STD_quant_start=0.000000;STD_quant_stop=1.397758;Kurtosis_quant_start=46.694151;Kurtosis_quant_stop=1.277671;SVTYPE=INS;SUPTYPE=AL;SVLEN=11;STRANDS=+-;STRANDS2=5361,85,5361,85;RE=5446;REF_strand=104806,81486;Strandbias_pval=0;AF=0.0292337 GT:DR:DV 0/0:180846:5446 +chr20 4685224 4 TTTTTTTTTTTTT N . STRANDBIAS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4685235;STD_quant_start=0.000000;STD_quant_stop=1.008186;Kurtosis_quant_start=5.881963;Kurtosis_quant_stop=6.521245;SVTYPE=DEL;SUPTYPE=AL,NR;SVLEN=-11;STRANDS=+-;STRANDS2=369,362,369,362;RE=731;REF_strand=104807,81503;Strandbias_pval=0.00191516;AF=0.00392357 GT:DR:DV 0/0:185579:731 +chr20 4685224 5 ACAGGGTCTTGGCCTA N . STRANDBIAS IMPRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4685276;STD_quant_start=27.880325;STD_quant_stop=3.446012;Kurtosis_quant_start=-2.263535;Kurtosis_quant_stop=-0.331955;SVTYPE=DEL;SUPTYPE=AL,NR;SVLEN=-52;STRANDS=+-;STRANDS2=24,41,24,41;RE=65;REF_strand=104814,81623;Strandbias_pval=0.00242262;AF=0.000348643 GT:DR:DV 0/0:186372:65 +chr20 4685308 6 N TTTTTTTTTTTTT . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4685312;STD_quant_start=6.708204;STD_quant_stop=6.512808;Kurtosis_quant_start=-1.560013;Kurtosis_quant_stop=-1.700246;SVTYPE=INS;SUPTYPE=AL;SVLEN=11;STRANDS=+-;STRANDS2=14,11,14,11;RE=25;REF_strand=104888,81967;Strandbias_pval=1;AF=0.000133794 GT:DR:DV 0/0:186830:25 +chr20 4685334 7 GCTCACTGCAGCCTCTACCTCCTGGGCTCAAGCAATCCTCCCATCTCAGCCTCCCCAGTAGCTGGGACTACAGGACTGTGCCACCGTTCCCAGC N . PASS IMPRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4685407;STD_quant_start=25.408660;STD_quant_stop=15.398052;Kurtosis_quant_start=-1.451975;Kurtosis_quant_stop=-1.008847;SVTYPE=DEL;SUPTYPE=AL;SVLEN=-73;STRANDS=+-;STRANDS2=9,3,9,3;RE=12;REF_strand=104892,82242;Strandbias_pval=0.249125;AF=6.41252e-05 GT:DR:DV 0/0:187122:12 +chr20 4685413 8 N TTTTTTTTTTT . STRANDBIAS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4685413;STD_quant_start=0.115470;STD_quant_stop=4.525483;Kurtosis_quant_start=1.123372;Kurtosis_quant_stop=-0.989658;SVTYPE=INS;SUPTYPE=AL;SVLEN=11;STRANDS=+-;STRANDS2=134,17,134,17;RE=151;REF_strand=104894,82410;Strandbias_pval=4.54894e-18;AF=0.000806176 GT:DR:DV 0/0:187153:151 +chr20 4685412 9 ATTTTTTTTAT N . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4685424;STD_quant_start=6.477457;STD_quant_stop=5.692474;Kurtosis_quant_start=-1.820652;Kurtosis_quant_stop=-1.510148;SVTYPE=DEL;SUPTYPE=AL;SVLEN=-12;STRANDS=+-;STRANDS2=60,34,60,34;RE=94;REF_strand=104894,82428;Strandbias_pval=0.1455;AF=0.00050181 GT:DR:DV 0/0:187228:94 +chr20 4685478 10 N GCCTGTCTTCATTTCAT . PASS IMPRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4685491;STD_quant_start=13.607125;STD_quant_stop=13.686040;Kurtosis_quant_start=-2.152028;Kurtosis_quant_stop=-2.118516;SVTYPE=INS;SUPTYPE=AL;SVLEN=13;STRANDS=+-;STRANDS2=18,9,18,9;RE=27;REF_strand=104896,82724;Strandbias_pval=0.333241;AF=0.000143908 GT:DR:DV 0/0:187593:27 +chr20 4685524 11 TACAGGCCTGAGCCACTGCACCTGGC N . PASS IMPRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4685546;STD_quant_start=7.880151;STD_quant_stop=10.319102;Kurtosis_quant_start=-1.915203;Kurtosis_quant_stop=-1.977764;SVTYPE=DEL;SUPTYPE=AL,NR;SVLEN=-22;STRANDS=+-;STRANDS2=33,29,33,29;RE=62;REF_strand=104898,82914;Strandbias_pval=0.702431;AF=0.000330117 GT:DR:DV 0/0:187750:62 +chr20 4685561 12 N ATCTTTTTGTTGTTCTGCGTTTACATT . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4685564;STD_quant_start=2.645751;STD_quant_stop=3.209361;Kurtosis_quant_start=-1.401297;Kurtosis_quant_stop=-1.599805;SVTYPE=INS;SUPTYPE=AL;SVLEN=12;STRANDS=+-;STRANDS2=10,11,10,11;RE=21;REF_strand=104898,83002;Strandbias_pval=0.512767;AF=0.000111762 GT:DR:DV 0/0:187879:21 +chr20 4685568 13 CATGCTTCCTAAACCTCTCACCC N . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4685597;STD_quant_start=4.197069;STD_quant_stop=4.795832;Kurtosis_quant_start=-1.931570;Kurtosis_quant_stop=-0.990923;SVTYPE=DEL;SUPTYPE=AL;SVLEN=-29;STRANDS=+-;STRANDS2=20,7,20,7;RE=27;REF_strand=104898,83082;Strandbias_pval=0.0792491;AF=0.000143632 GT:DR:DV 0/0:187953:27 +chr20 4685605 14 N AGAAACTGAAGGAAGAAGGAGGAGGAG . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4685610;STD_quant_start=7.549834;STD_quant_stop=7.032393;Kurtosis_quant_start=-1.923065;Kurtosis_quant_stop=-1.769579;SVTYPE=INS;SUPTYPE=AL;SVLEN=13;STRANDS=+-;STRANDS2=14,9,14,9;RE=23;REF_strand=104898,83178;Strandbias_pval=0.679359;AF=0.000122291 GT:DR:DV 0/0:188053:23 +chr20 4685652 15 N TTCTCATTTTTCCTTAGCCTGCTTGCTCTG . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4685658;STD_quant_start=7.918333;STD_quant_stop=4.324350;Kurtosis_quant_start=-2.033978;Kurtosis_quant_stop=-1.720878;SVTYPE=INS;SUPTYPE=AL;SVLEN=21;STRANDS=+-;STRANDS2=11,10,11,10;RE=21;REF_strand=104900,83341;Strandbias_pval=0.827694;AF=0.000111559 GT:DR:DV 0/0:188220:21 +chr20 4685693 16 ATCCCCCTCCCTCTAA N . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4685709;STD_quant_start=1.961161;STD_quant_stop=0.733799;Kurtosis_quant_start=0.767717;Kurtosis_quant_stop=0.884723;SVTYPE=DEL;SUPTYPE=AL;SVLEN=-16;STRANDS=+-;STRANDS2=11,16,11,16;RE=27;REF_strand=104900,83504;Strandbias_pval=0.125367;AF=0.000143309 GT:DR:DV 0/0:188377:27 +chr20 4685719 17 N TCCCCCCCCTC . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4685722;STD_quant_start=7.596052;STD_quant_stop=7.668116;Kurtosis_quant_start=-2.037716;Kurtosis_quant_stop=-1.695322;SVTYPE=INS;SUPTYPE=AL;SVLEN=11;STRANDS=+-;STRANDS2=9,12,9,12;RE=21;REF_strand=104900,83587;Strandbias_pval=0.275261;AF=0.000111414 GT:DR:DV 0/0:188466:21 +chr20 4685787 18 N CCCCCCCCCCCCCCCC . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4685797;STD_quant_start=6.549809;STD_quant_stop=5.234501;Kurtosis_quant_start=-1.993791;Kurtosis_quant_stop=-1.620499;SVTYPE=INS;SUPTYPE=AL;SVLEN=11;STRANDS=+-;STRANDS2=13,8,13,8;RE=21;REF_strand=104900,83810;Strandbias_pval=0.663087;AF=0.000111282 GT:DR:DV 0/0:188689:21 +chr20 4685812 19 CTCAGGTAATGTGC N . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4685826;STD_quant_start=1.702939;STD_quant_stop=1.732051;Kurtosis_quant_start=1.835409;Kurtosis_quant_stop=1.594983;SVTYPE=DEL;SUPTYPE=AL;SVLEN=-14;STRANDS=+-;STRANDS2=10,9,10,9;RE=19;REF_strand=104900,83909;Strandbias_pval=0.820938;AF=0.000100631 GT:DR:DV 0/0:188790:19 +chr20 4685835 20 N TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT . STRANDBIAS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4685858;STD_quant_start=6.341177;STD_quant_stop=8.711759;Kurtosis_quant_start=-1.827946;Kurtosis_quant_stop=-1.880209;SVTYPE=INS;SUPTYPE=AL;SVLEN=11;STRANDS=+-;STRANDS2=34,4,34,4;RE=38;REF_strand=104900,83990;Strandbias_pval=9.93921e-06;AF=0.000201175 GT:DR:DV 0/0:188852:38 +chr20 4685835 21 TTTTTAAACGGAGCGCATTTTTCTCATTTGTTAATATCACCACCTAAATCATCTC N . PASS IMPRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4685927;STD_quant_start=9.477022;STD_quant_stop=25.738398;Kurtosis_quant_start=-1.651526;Kurtosis_quant_stop=-2.098104;SVTYPE=DEL;SUPTYPE=AL;SVLEN=-92;STRANDS=+-;STRANDS2=48,38,48,38;RE=86;REF_strand=104897,84101;Strandbias_pval=1;AF=0.000455031 GT:DR:DV 0/0:188912:86 +chr20 4685919 22 GAAGGAAGGAACA N . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4685938;STD_quant_start=1.632993;STD_quant_stop=3.286335;Kurtosis_quant_start=0.397663;Kurtosis_quant_stop=-0.290084;SVTYPE=DEL;SUPTYPE=AL;SVLEN=-19;STRANDS=+-;STRANDS2=12,19,12,19;RE=31;REF_strand=104893,84264;Strandbias_pval=0.0708274;AF=0.000163885 GT:DR:DV 0/0:189126:31 +chr20 4685944 23 TCCTTTCTACGCC N . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4685959;STD_quant_start=5.364492;STD_quant_stop=5.978356;Kurtosis_quant_start=-0.120485;Kurtosis_quant_stop=-0.419259;SVTYPE=DEL;SUPTYPE=AL;SVLEN=-15;STRANDS=+-;STRANDS2=34,20,34,20;RE=54;REF_strand=104866,84361;Strandbias_pval=0.277016;AF=0.000285372 GT:DR:DV 0/0:189173:54 +chr20 4686035 24 N CTCTAATAATAATATG . PASS IMPRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4686044;STD_quant_start=12.206556;STD_quant_stop=8.288546;Kurtosis_quant_start=-0.985283;Kurtosis_quant_stop=-1.333246;SVTYPE=INS;SUPTYPE=AL;SVLEN=15;STRANDS=+-;STRANDS2=10,1,10,1;RE=11;REF_strand=104473,84638;Strandbias_pval=0.0286913;AF=5.81669e-05 GT:DR:DV 0/0:189100:11 +chr20 4686014 25 AGCAAAATTTT N . STRANDBIAS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4686034;STD_quant_start=4.476792;STD_quant_stop=4.344537;Kurtosis_quant_start=-1.557400;Kurtosis_quant_stop=-1.120073;SVTYPE=DEL;SUPTYPE=AL;SVLEN=-20;STRANDS=+-;STRANDS2=17,31,17,31;RE=48;REF_strand=104540,84588;Strandbias_pval=0.00826446;AF=0.000253796 GT:DR:DV 0/0:189080:48 +chr20 4686090 26 N TTTTTTTTTTTTTTTTTTT . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4686096;STD_quant_start=3.911521;STD_quant_stop=5.108816;Kurtosis_quant_start=-1.760952;Kurtosis_quant_stop=-1.685478;SVTYPE=INS;SUPTYPE=AL;SVLEN=12;STRANDS=+-;STRANDS2=14,6,14,6;RE=20;REF_strand=104232,84797;Strandbias_pval=0.260655;AF=0.000105804 GT:DR:DV 0/0:189009:20 +chr20 4686137 27 CCGAATTTCCAA N . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4686153;STD_quant_start=4.396969;STD_quant_stop=2.909754;Kurtosis_quant_start=-0.870860;Kurtosis_quant_stop=0.288634;SVTYPE=DEL;SUPTYPE=AL;SVLEN=-16;STRANDS=+-;STRANDS2=12,18,12,18;RE=30;REF_strand=103958,84935;Strandbias_pval=0.102322;AF=0.00015882 GT:DR:DV 0/0:188863:30 +chr20 4686249 28 N TTTTTTTTTTT . STRANDBIAS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4686249;STD_quant_start=0.745356;STD_quant_stop=4.490731;Kurtosis_quant_start=-0.542114;Kurtosis_quant_stop=-1.136090;SVTYPE=INS;SUPTYPE=AL;SVLEN=11;STRANDS=+-;STRANDS2=29,7,29,7;RE=36;REF_strand=103338,85310;Strandbias_pval=0.00210876;AF=0.000190832 GT:DR:DV 0/0:188612:36 +chr20 4686284 29 GCAGCGCTGCACCCTTTAACTTAAA N . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4686310;STD_quant_start=4.415880;STD_quant_stop=6.292853;Kurtosis_quant_start=3.267286;Kurtosis_quant_stop=-0.210596;SVTYPE=DEL;SUPTYPE=AL,NR;SVLEN=-26;STRANDS=+-;STRANDS2=5,11,5,11;RE=16;REF_strand=103038,85481;Strandbias_pval=0.0779362;AF=8.48721e-05 GT:DR:DV 0/0:188503:16 +chr20 4686305 30 N TCCCGAGCAATGCG . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4686307;STD_quant_start=7.523297;STD_quant_stop=7.463243;Kurtosis_quant_start=-1.080943;Kurtosis_quant_stop=-0.809562;SVTYPE=INS;SUPTYPE=AL;SVLEN=17;STRANDS=+-;STRANDS2=7,10,7,10;RE=17;REF_strand=102977,85513;Strandbias_pval=0.331901;AF=9.01905e-05 GT:DR:DV 0/0:188473:17 +chr20 4686369 31 N GCTGCTGCGGAAGAAGCT . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4686381;STD_quant_start=6.480741;STD_quant_stop=8.862193;Kurtosis_quant_start=-1.959595;Kurtosis_quant_stop=-1.752628;SVTYPE=INS;SUPTYPE=AL;SVLEN=11;STRANDS=+-;STRANDS2=10,16,10,16;RE=26;REF_strand=102563,85737;Strandbias_pval=0.116522;AF=0.000138078 GT:DR:DV 0/0:188274:26 +chr20 4686411 32 CCCCGCGTCCCTC N . STRANDBIAS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4686437;STD_quant_start=6.283311;STD_quant_stop=8.860023;Kurtosis_quant_start=-1.485112;Kurtosis_quant_stop=-2.048321;SVTYPE=DEL;SUPTYPE=AL;SVLEN=-26;STRANDS=+-;STRANDS2=88,113,88,113;RE=201;REF_strand=102278,85895;Strandbias_pval=0.00287042;AF=0.00106817 GT:DR:DV 0/0:187972:201 +chr20 4686460 33 CCAGTCGCTGACAGCCGC N . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4686476;STD_quant_start=7.290554;STD_quant_stop=6.296997;Kurtosis_quant_start=-0.598536;Kurtosis_quant_stop=-0.768597;SVTYPE=DEL;SUPTYPE=AL,NR;SVLEN=-16;STRANDS=+-;STRANDS2=47,46,47,46;RE=93;REF_strand=102044,86031;Strandbias_pval=0.532458;AF=0.000494484 GT:DR:DV 0/0:187982:93 +chr20 4686423 34 N CACACACGGGCCATTGCCG . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4686448;STD_quant_start=7.611910;STD_quant_stop=8.303082;Kurtosis_quant_start=-1.873606;Kurtosis_quant_stop=-1.894533;SVTYPE=INS;SUPTYPE=AL;SVLEN=12;STRANDS=+-;STRANDS2=14,20,14,20;RE=34;REF_strand=102220,85938;Strandbias_pval=0.167475;AF=0.000180699 GT:DR:DV 0/0:188124:34 +chr20 4686486 35 CTTCTCCTCTC N . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4686497;STD_quant_start=0.675664;STD_quant_stop=1.750776;Kurtosis_quant_start=0.151270;Kurtosis_quant_stop=1.964863;SVTYPE=DEL;SUPTYPE=AL;SVLEN=-11;STRANDS=+-;STRANDS2=52,41,52,41;RE=93;REF_strand=101953,86089;Strandbias_pval=0.756119;AF=0.00049457 GT:DR:DV 0/0:187949:93 +chr20 4686522 36 N GCGCTTTGCCGCGCGCGCTGCG . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4686530;STD_quant_start=8.421203;STD_quant_stop=8.920949;Kurtosis_quant_start=-1.724746;Kurtosis_quant_stop=-1.925360;SVTYPE=INS;SUPTYPE=AL;SVLEN=11;STRANDS=+-;STRANDS2=15,9,15,9;RE=24;REF_strand=101813,86202;Strandbias_pval=0.539823;AF=0.000127649 GT:DR:DV 0/0:187991:24 +chr20 4686557 37 GGGGGCCGAGTGAGGACCCCGGGCCTCGGGTCCCAGGCGCAAGGGTGCCCGGCCGGGCGGGGTCGGGACCCCAGTGAGGAGGGGCCG N . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4686645;STD_quant_start=9.919677;STD_quant_stop=9.132360;Kurtosis_quant_start=-1.502438;Kurtosis_quant_stop=0.599019;SVTYPE=DEL;SUPTYPE=AL;SVLEN=-88;STRANDS=+-;STRANDS2=5,9,5,9;RE=14;REF_strand=101467,86479;Strandbias_pval=0.189371;AF=7.44895e-05 GT:DR:DV 0/0:187932:14 +chr20 4686637 38 GGAGGGGCCGG N . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4686653;STD_quant_start=6.509071;STD_quant_stop=6.109010;Kurtosis_quant_start=-1.591669;Kurtosis_quant_stop=-1.847614;SVTYPE=DEL;SUPTYPE=AL,NR;SVLEN=-16;STRANDS=+-;STRANDS2=118,133,118,133;RE=251;REF_strand=101274,86647;Strandbias_pval=0.0311372;AF=0.00133567 GT:DR:DV 0/0:187670:251 +chr20 4686640 39 N AGGAGGAGGAGTC . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4686643;STD_quant_start=7.221001;STD_quant_stop=7.796519;Kurtosis_quant_start=-1.574661;Kurtosis_quant_stop=-1.513590;SVTYPE=INS;SUPTYPE=AL;SVLEN=13;STRANDS=+-;STRANDS2=19,9,19,9;RE=28;REF_strand=101301,86625;Strandbias_pval=0.18389;AF=0.000148995 GT:DR:DV 0/0:187898:28 +chr20 4686675 40 TCGGGCCTGCCCGGCTGCGCTGGTCT N . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4686702;STD_quant_start=3.562254;STD_quant_stop=6.119500;Kurtosis_quant_start=-1.685544;Kurtosis_quant_stop=-1.479437;SVTYPE=DEL;SUPTYPE=AL,NR;SVLEN=-27;STRANDS=+-;STRANDS2=38,20,38,20;RE=58;REF_strand=101111,86801;Strandbias_pval=0.0864537;AF=0.000308655 GT:DR:DV 0/0:187854:58 +chr20 4686693 41 N GCCACACGCCTGGCCATGCGCTGC . PASS IMPRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4686706;STD_quant_start=11.366618;STD_quant_stop=8.619745;Kurtosis_quant_start=-2.119231;Kurtosis_quant_stop=-1.933757;SVTYPE=INS;SUPTYPE=AL;SVLEN=11;STRANDS=+-;STRANDS2=9,12,9,12;RE=21;REF_strand=101076,86839;Strandbias_pval=0.383237;AF=0.000111753 GT:DR:DV 0/0:187894:21 +chr20 4686737 42 CGGAGCCCCGTTAGGGAGGTCGGTGGCGCCGGGGTGTCTCAGCGCCC N . PASS IMPRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4686835;STD_quant_start=26.517918;STD_quant_stop=24.433583;Kurtosis_quant_start=-0.815110;Kurtosis_quant_stop=0.235425;SVTYPE=DEL;SUPTYPE=AL;SVLEN=-98;STRANDS=+-;STRANDS2=4,6,4,6;RE=10;REF_strand=100637,87133;Strandbias_pval=0.529397;AF=5.32566e-05 GT:DR:DV 0/0:187760:10 +chr20 4686828 43 N AAGGCGGGTGCG . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4686829;STD_quant_start=5.540758;STD_quant_stop=6.488451;Kurtosis_quant_start=-0.796598;Kurtosis_quant_stop=-1.499531;SVTYPE=INS;SUPTYPE=AL;SVLEN=28;STRANDS=+-;STRANDS2=5,14,5,14;RE=19;REF_strand=100434,87274;Strandbias_pval=0.0207425;AF=0.000101221 GT:DR:DV 0/0:187689:19 +chr20 4686805 44 TGGCGCCGGGGTGTCTCAGCGCCCCCTGC N . PASS IMPRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4686842;STD_quant_start=11.217483;STD_quant_stop=5.794811;Kurtosis_quant_start=-1.707219;Kurtosis_quant_stop=-1.610205;SVTYPE=DEL;SUPTYPE=AL;SVLEN=-37;STRANDS=+-;STRANDS2=124,115,124,115;RE=239;REF_strand=100454,87264;Strandbias_pval=0.649788;AF=0.00127319 GT:DR:DV 0/0:187479:239 +chr20 4686928 45 GGGAGGGGCGCCTGGGGGC N . STRANDBIAS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4686943;STD_quant_start=7.271520;STD_quant_stop=7.969809;Kurtosis_quant_start=-1.428060;Kurtosis_quant_stop=-1.384092;SVTYPE=DEL;SUPTYPE=AL;SVLEN=-15;STRANDS=+-;STRANDS2=123,214,123,214;RE=337;REF_strand=99888,87636;Strandbias_pval=6.90604e-10;AF=0.0017971 GT:DR:DV 0/0:187187:337 +chr20 4686963 46 CGTTGGCCGCCCCT N . STRANDBIAS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4686979;STD_quant_start=5.601339;STD_quant_stop=4.555217;Kurtosis_quant_start=-1.630635;Kurtosis_quant_stop=-0.943511;SVTYPE=DEL;SUPTYPE=AL,NR;SVLEN=-16;STRANDS=+-;STRANDS2=47,18,47,18;RE=65;REF_strand=99717,87823;Strandbias_pval=0.00180972;AF=0.000346593 GT:DR:DV 0/0:187475:65 +chr20 4686964 47 N GCAGAGGCAGGAGGCGCC . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4686970;STD_quant_start=8.845230;STD_quant_stop=9.172942;Kurtosis_quant_start=-1.952054;Kurtosis_quant_stop=-1.860983;SVTYPE=INS;SUPTYPE=AL;SVLEN=11;STRANDS=+-;STRANDS2=27,15,27,15;RE=42;REF_strand=99738,87802;Strandbias_pval=0.165692;AF=0.000223952 GT:DR:DV 0/0:187498:42 +chr20 4687035 48 AGAGGGTGCTTGGGGGGATGGAGAGAGGGGCGCCCGCCGGGGGAGTTCCGGGAGCCTCGGT N . PASS IMPRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4687100;STD_quant_start=11.755850;STD_quant_stop=9.104944;Kurtosis_quant_start=-0.304299;Kurtosis_quant_stop=-0.647176;SVTYPE=DEL;SUPTYPE=AL,NR;SVLEN=-65;STRANDS=+-;STRANDS2=5,7,5,7;RE=12;REF_strand=99285,88267;Strandbias_pval=0.566004;AF=6.39823e-05 GT:DR:DV 0/0:187540:12 +chr20 4687051 49 N GGGGGGGGGGGGGGGGGGG . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4687056;STD_quant_start=7.483315;STD_quant_stop=6.985700;Kurtosis_quant_start=-1.706525;Kurtosis_quant_stop=-1.595314;SVTYPE=INS;SUPTYPE=AL;SVLEN=11;STRANDS=+-;STRANDS2=22,9,22,9;RE=31;REF_strand=99349,88205;Strandbias_pval=0.0484956;AF=0.000165286 GT:DR:DV 0/0:187523:31 +chr20 4687064 50 AGGGGCGCCCGCC N . STRANDBIAS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4687078;STD_quant_start=4.492793;STD_quant_stop=4.721895;Kurtosis_quant_start=-1.437022;Kurtosis_quant_stop=-0.754098;SVTYPE=DEL;SUPTYPE=AL,NR;SVLEN=-14;STRANDS=+-;STRANDS2=53,110,53,110;RE=163;REF_strand=99272,88295;Strandbias_pval=2.32173e-07;AF=0.000869023 GT:DR:DV 0/0:187404:163 +chr20 4687131 51 N GCCCCTTGCGCCGCT . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4687138;STD_quant_start=8.639853;STD_quant_stop=8.683995;Kurtosis_quant_start=-1.940362;Kurtosis_quant_stop=-1.804865;SVTYPE=INS;SUPTYPE=AL;SVLEN=13;STRANDS=+-;STRANDS2=18,16,18,16;RE=34;REF_strand=99035,88562;Strandbias_pval=1;AF=0.00018124 GT:DR:DV 0/0:187563:34 +chr20 4687107 52 CGCAGCTGCAGCGTTCCTCCCGGGA N . PASS IMPRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4687149;STD_quant_start=13.508209;STD_quant_stop=7.339477;Kurtosis_quant_start=-1.982890;Kurtosis_quant_stop=-1.656688;SVTYPE=DEL;SUPTYPE=AL,NR;SVLEN=-42;STRANDS=+-;STRANDS2=58,48,58,48;RE=106;REF_strand=99037,88528;Strandbias_pval=0.698631;AF=0.000565137 GT:DR:DV 0/0:187459:106 +chr20 4687222 53 N CCCTCCCTCCCTCTCCGCCCT . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4687227;STD_quant_start=5.608435;STD_quant_stop=5.760366;Kurtosis_quant_start=-1.804722;Kurtosis_quant_stop=-1.953711;SVTYPE=INS;SUPTYPE=AL;SVLEN=11;STRANDS=+-;STRANDS2=13,10,13,10;RE=23;REF_strand=98608,88620;Strandbias_pval=0.835451;AF=0.000122845 GT:DR:DV 0/0:187205:23 +chr20 4687270 54 N GGGGGGGGGGGGGGGGG . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4687277;STD_quant_start=9.490597;STD_quant_stop=9.137833;Kurtosis_quant_start=-1.469964;Kurtosis_quant_stop=-1.731014;SVTYPE=INS;SUPTYPE=AL;SVLEN=11;STRANDS=+-;STRANDS2=15,13,15,13;RE=28;REF_strand=98360,88622;Strandbias_pval=1;AF=0.000149747 GT:DR:DV 0/0:186954:28 +chr20 4687275 55 CCGGGGAGGCCC N . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4687287;STD_quant_start=6.346801;STD_quant_stop=6.667058;Kurtosis_quant_start=-1.393283;Kurtosis_quant_stop=-1.501549;SVTYPE=DEL;SUPTYPE=AL;SVLEN=-12;STRANDS=+-;STRANDS2=164,134,164,134;RE=298;REF_strand=98324,88622;Strandbias_pval=0.416628;AF=0.00159404 GT:DR:DV 0/0:186648:298 +chr20 4687315 56 N CTGCCGCCGCGGACAGGTGCAGCGGCGGCGGGCGGCCAGCAGGGGCCCCAACTTGTCAGGGT . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4687327;STD_quant_start=6.685806;STD_quant_stop=8.215838;Kurtosis_quant_start=-1.076909;Kurtosis_quant_stop=-0.779172;SVTYPE=INS;SUPTYPE=AL;SVLEN=11;STRANDS=+-;STRANDS2=3,11,3,11;RE=14;REF_strand=98189,88622;Strandbias_pval=0.0289998;AF=7.49421e-05 GT:DR:DV 0/0:186797:14 +chr20 4687420 57 GGCTCCAAGGAACAACCAGCCTCGGATGAC N . PASS IMPRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4687464;STD_quant_start=13.416408;STD_quant_stop=8.124038;Kurtosis_quant_start=-2.001488;Kurtosis_quant_stop=-0.910864;SVTYPE=DEL;SUPTYPE=AL,NR;SVLEN=-44;STRANDS=+-;STRANDS2=9,8,9,8;RE=17;REF_strand=97743,88622;Strandbias_pval=1;AF=9.12188e-05 GT:DR:DV 0/0:186348:17 +chr20 4687436 58 N CGGCGGCAGCTATGG . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4687437;STD_quant_start=7.752419;STD_quant_stop=8.000000;Kurtosis_quant_start=-1.559791;Kurtosis_quant_stop=-1.206510;SVTYPE=INS;SUPTYPE=AL;SVLEN=14;STRANDS=+-;STRANDS2=6,11,6,11;RE=17;REF_strand=97773,88622;Strandbias_pval=0.223976;AF=9.12042e-05 GT:DR:DV 0/0:186378:17 +chr20 4687454 59 GCGGCAGGCGCCTTCAC N . PASS IMPRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4687496;STD_quant_start=19.321461;STD_quant_stop=11.697888;Kurtosis_quant_start=-1.947753;Kurtosis_quant_stop=-1.804670;SVTYPE=DEL;SUPTYPE=AL;SVLEN=-42;STRANDS=+-;STRANDS2=81,57,81,57;RE=138;REF_strand=97605,88622;Strandbias_pval=0.147654;AF=0.000741031 GT:DR:DV 0/0:186089:138 +chr20 4687529 60 N GTCACAGAGAGCCGC . PASS IMPRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4687532;STD_quant_start=11.224972;STD_quant_stop=9.899495;Kurtosis_quant_start=-1.022882;Kurtosis_quant_stop=-1.134611;SVTYPE=INS;SUPTYPE=AL;SVLEN=17;STRANDS=+-;STRANDS2=6,6,6,6;RE=12;REF_strand=97360,88620;Strandbias_pval=1;AF=6.45231e-05 GT:DR:DV 0/0:185968:12 +chr20 4687579 61 TAGGAAATAGATTTTTTTTT N . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4687600;STD_quant_start=7.117610;STD_quant_stop=4.979202;Kurtosis_quant_start=-0.928619;Kurtosis_quant_stop=-1.467682;SVTYPE=DEL;SUPTYPE=AL,NR;SVLEN=-21;STRANDS=+-;STRANDS2=47,60,47,60;RE=107;REF_strand=97041,88620;Strandbias_pval=0.0994266;AF=0.000576319 GT:DR:DV 0/0:185554:107 +chr20 4687590 62 N ATTTTTTTTTTTTTTT . STRANDBIAS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4687591;STD_quant_start=0.000000;STD_quant_stop=1.484382;Kurtosis_quant_start=1.016702;Kurtosis_quant_stop=-0.353406;SVTYPE=INS;SUPTYPE=AL;SVLEN=11;STRANDS=+-;STRANDS2=110,9,110,9;RE=119;REF_strand=97005,88620;Strandbias_pval=1.56932e-21;AF=0.000641077 GT:DR:DV 0/0:185506:119 +chr20 4687644 63 N ACCAATATAGCTGTTTCGTGTATTTTGT . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4687648;STD_quant_start=7.280110;STD_quant_stop=6.655825;Kurtosis_quant_start=-2.097407;Kurtosis_quant_stop=-1.781270;SVTYPE=INS;SUPTYPE=AL;SVLEN=20;STRANDS=+-;STRANDS2=12,9,12,9;RE=21;REF_strand=96831,88616;Strandbias_pval=0.670153;AF=0.00011324 GT:DR:DV 0/0:185426:21 +chr20 4687662 64 TTTGTTTCCTAGCCTCCAGATTCTCACACAACACAGTGCAGTTTCACTGCTGTAATGATGAGGATCTTCATGGCCGCGTTATTTTCTTG N . PASS IMPRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4687749;STD_quant_start=13.560973;STD_quant_stop=23.828554;Kurtosis_quant_start=-0.500725;Kurtosis_quant_stop=-0.751946;SVTYPE=DEL;SUPTYPE=AL;SVLEN=-87;STRANDS=+-;STRANDS2=6,4,6,4;RE=10;REF_strand=96549,88613;Strandbias_pval=0.756153;AF=5.40068e-05 GT:DR:DV 0/0:185152:10 +chr20 4687726 65 TTCATGGCCGCG N . STRANDBIAS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4687740;STD_quant_start=3.587728;STD_quant_stop=3.886202;Kurtosis_quant_start=-1.201868;Kurtosis_quant_stop=-1.012534;SVTYPE=DEL;SUPTYPE=AL;SVLEN=-14;STRANDS=+-;STRANDS2=56,23,56,23;RE=79;REF_strand=96445,88614;Strandbias_pval=0.000966226;AF=0.000426891 GT:DR:DV 0/0:184980:79 +chr20 4687830 66 TTAAGGATTTT N . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4687850;STD_quant_start=4.954796;STD_quant_stop=5.296225;Kurtosis_quant_start=-0.684968;Kurtosis_quant_stop=0.004459;SVTYPE=DEL;SUPTYPE=AL;SVLEN=-20;STRANDS=+-;STRANDS2=24,17,24,17;RE=41;REF_strand=95963,88603;Strandbias_pval=0.437332;AF=0.000222143 GT:DR:DV 0/0:184525:41 +chr20 4687876 67 ATCAAAAACATAGGAACAGGG N . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4687891;STD_quant_start=3.497252;STD_quant_stop=3.932116;Kurtosis_quant_start=-1.627058;Kurtosis_quant_stop=-1.499194;SVTYPE=DEL;SUPTYPE=AL;SVLEN=-15;STRANDS=+-;STRANDS2=9,18,9,18;RE=27;REF_strand=95750,88599;Strandbias_pval=0.0562685;AF=0.000146461 GT:DR:DV 0/0:184322:27 +chr20 4687902 68 N . PASS IMPRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4687965;STD_quant_start=14.472675;STD_quant_stop=14.135505;Kurtosis_quant_start=-1.868761;Kurtosis_quant_stop=-1.924140;SVTYPE=DEL;SUPTYPE=AL;SVLEN=-63;STRANDS=+-;STRANDS2=50,47,50,47;RE=97;REF_strand=95435,88587;Strandbias_pval=1;AF=0.000527111 GT:DR:DV 0/0:183925:97 +chr20 4688011 69 N AAAAAAAAAAA . STRANDBIAS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4688011;STD_quant_start=0.000000;STD_quant_stop=2.340126;Kurtosis_quant_start=-0.888557;Kurtosis_quant_stop=-1.060011;SVTYPE=INS;SUPTYPE=AL;SVLEN=11;STRANDS=+-;STRANDS2=7,35,7,35;RE=42;REF_strand=94694,88398;Strandbias_pval=3.42828e-06;AF=0.000229393 GT:DR:DV 0/0:183050:42 +chr20 4687999 70 N . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4688015;STD_quant_start=3.401680;STD_quant_stop=3.422614;Kurtosis_quant_start=-1.624204;Kurtosis_quant_stop=-1.871784;SVTYPE=DEL;SUPTYPE=AL;SVLEN=-16;STRANDS=+-;STRANDS2=10,18,10,18;RE=28;REF_strand=94772,88452;Strandbias_pval=0.128848;AF=0.000152818 GT:DR:DV 0/0:183196:28 diff --git a/SVs_sniffles/vcf/58398_bodySnif.vcf b/SVs_sniffles/vcf/58398_bodySnif.vcf new file mode 100644 index 0000000..ebefbe5 --- /dev/null +++ b/SVs_sniffles/vcf/58398_bodySnif.vcf @@ -0,0 +1,36 @@ +##fileformat=VCFv4.1 +##source=Sniffles +##fileDate=20210810:59:12 AMef_minus +##contig= +##ALT= +##ALT= +##ALT= +##ALT= +##ALT= +##ALT= +##FILTER= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##FORMAT= +##FORMAT= +##FORMAT= +#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT bamfilt/58398_f.bam diff --git a/SVs_sniffles/vcf/58398_promoterSnif.vcf b/SVs_sniffles/vcf/58398_promoterSnif.vcf new file mode 100644 index 0000000..73da196 --- /dev/null +++ b/SVs_sniffles/vcf/58398_promoterSnif.vcf @@ -0,0 +1,86 @@ +##fileformat=VCFv4.1 +##source=Sniffles +##fileDate=20210811:54:59 AMef_minus +##contig= +##ALT= +##ALT= +##ALT= +##ALT= +##ALT= +##ALT= +##FILTER= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##FORMAT= +##FORMAT= +##FORMAT= +#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT promoterbamfilt/58398_f.bam +chr20 4685112 0 CTGGCTTCTCCTGTCTCT N . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4685128;STD_quant_start=5.279678;STD_quant_stop=4.782782;Kurtosis_quant_start=-1.878171;Kurtosis_quant_stop=-1.843780;SVTYPE=DEL;SUPTYPE=AL;SVLEN=-16;STRANDS=+-;STRANDS2=21,12,21,12;RE=33;REF_strand=68359,35597;Strandbias_pval=0.854841;AF=0.000317442 GT:DR:DV 0/0:103923:33 +chr20 4685146 1 CTCCCCTGCAACT N . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4685159;STD_quant_start=4.562695;STD_quant_stop=3.931227;Kurtosis_quant_start=-1.518755;Kurtosis_quant_stop=-0.902202;SVTYPE=DEL;SUPTYPE=AL;SVLEN=-13;STRANDS=+-;STRANDS2=13,9,13,9;RE=22;REF_strand=68388,35684;Strandbias_pval=0.507637;AF=0.000211392 GT:DR:DV 0/0:104050:22 +chr20 4685224 2 N TTTTTTTTTTT . STRANDBIAS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4685224;STD_quant_start=0.000000;STD_quant_stop=1.183791;Kurtosis_quant_start=186.161765;Kurtosis_quant_stop=2.285904;SVTYPE=INS;SUPTYPE=AL;SVLEN=11;STRANDS=+-;STRANDS2=3201,33,3201,33;RE=3234;REF_strand=68408,35836;Strandbias_pval=0;AF=0.0310234 GT:DR:DV 0/0:101010:3234 +chr20 4685224 3 TTTTTTTTTTTTT N . STRANDBIAS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4685235;STD_quant_start=0.000000;STD_quant_stop=0.881917;Kurtosis_quant_start=3.692424;Kurtosis_quant_stop=2.704147;SVTYPE=DEL;SUPTYPE=AL,NR;SVLEN=-11;STRANDS=+-;STRANDS2=274,195,274,195;RE=469;REF_strand=68409,35848;Strandbias_pval=0.00128529;AF=0.0044985 GT:DR:DV 0/0:103788:469 +chr20 4685224 4 N TTTTTTTTTTTTTTTTTTTTTTTTTTTTT . STRANDBIAS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4685224;STD_quant_start=0.000000;STD_quant_stop=2.027419;Kurtosis_quant_start=7.100426;Kurtosis_quant_stop=0.233165;SVTYPE=INS;SUPTYPE=AL;SVLEN=23;STRANDS=+-;STRANDS2=325,1,325,1;RE=326;REF_strand=68408,35836;Strandbias_pval=6.40909e-58;AF=0.00312728 GT:DR:DV 0/0:103918:326 +chr20 4685242 5 N TTTTTTTTTTTTTC . STRANDBIAS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4685243;STD_quant_start=1.131371;STD_quant_stop=1.777639;Kurtosis_quant_start=0.704176;Kurtosis_quant_stop=-0.348482;SVTYPE=INS;SUPTYPE=AL;SVLEN=11;STRANDS=+-;STRANDS2=44,6,44,6;RE=50;REF_strand=68412,35895;Strandbias_pval=0.000493411;AF=0.000479354 GT:DR:DV 0/0:104257:50 +chr20 4685391 6 ACTGTGCCACCGTTCCCA N . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4685411;STD_quant_start=4.266146;STD_quant_stop=2.529822;Kurtosis_quant_start=1.420041;Kurtosis_quant_stop=-0.788227;SVTYPE=DEL;SUPTYPE=AL;SVLEN=-20;STRANDS=+-;STRANDS2=13,4,13,4;RE=17;REF_strand=68453,36224;Strandbias_pval=0.448027;AF=0.000162404 GT:DR:DV 0/0:104660:17 +chr20 4685413 7 N TTTTTTTTTTTTT . STRANDBIAS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4685422;STD_quant_start=0.000000;STD_quant_stop=3.363406;Kurtosis_quant_start=1.915052;Kurtosis_quant_stop=1.170464;SVTYPE=INS;SUPTYPE=AL;SVLEN=11;STRANDS=+-;STRANDS2=59,6,59,6;RE=65;REF_strand=68454,36257;Strandbias_pval=3.0368e-06;AF=0.000620756 GT:DR:DV 0/0:104646:65 +chr20 4685422 8 N TTTTTTACACACAC . STRANDBIAS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4685422;STD_quant_start=0.730297;STD_quant_stop=1.341641;Kurtosis_quant_start=-1.694847;Kurtosis_quant_stop=0.454255;SVTYPE=INS;SUPTYPE=AL;SVLEN=22;STRANDS=+-;STRANDS2=29,2,29,2;RE=31;REF_strand=68454,36268;Strandbias_pval=0.000454269;AF=0.000296022 GT:DR:DV 0/0:104691:31 +chr20 4685413 9 ATTTTTTTTATT N . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4685424;STD_quant_start=1.365151;STD_quant_stop=1.381699;Kurtosis_quant_start=-1.342261;Kurtosis_quant_stop=-0.800467;SVTYPE=DEL;SUPTYPE=AL,NR;SVLEN=-11;STRANDS=+-;STRANDS2=32,13,32,13;RE=45;REF_strand=68454,36259;Strandbias_pval=0.531013;AF=0.000429746 GT:DR:DV 0/0:104668:45 +chr20 4685442 10 N TTTTTAAAAAAA . PASS IMPRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4685454;STD_quant_start=10.812801;STD_quant_stop=10.456258;Kurtosis_quant_start=-2.172929;Kurtosis_quant_stop=-2.237781;SVTYPE=INS;SUPTYPE=AL;SVLEN=11;STRANDS=+-;STRANDS2=19,6,19,6;RE=25;REF_strand=68454,36315;Strandbias_pval=0.300521;AF=0.00023862 GT:DR:DV 0/0:104744:25 +chr20 4685475 11 TCAAGCAATCT N . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4685490;STD_quant_start=6.610016;STD_quant_stop=5.850707;Kurtosis_quant_start=-1.897191;Kurtosis_quant_stop=-1.888881;SVTYPE=DEL;SUPTYPE=AL;SVLEN=-15;STRANDS=+-;STRANDS2=21,6,21,6;RE=27;REF_strand=68454,36358;Strandbias_pval=0.225485;AF=0.000257604 GT:DR:DV 0/0:104785:27 +chr20 4685558 12 N CCGCCCCCCTTTTGCCTGCCTAAACCTGCACCTGCACACCACTGCACCTG . PASS IMPRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4685578;STD_quant_start=15.984367;STD_quant_stop=12.825755;Kurtosis_quant_start=-1.161139;Kurtosis_quant_stop=-1.342397;SVTYPE=INS;SUPTYPE=AL;SVLEN=11;STRANDS=+-;STRANDS2=7,4,7,4;RE=11;REF_strand=68454,36511;Strandbias_pval=1;AF=0.000104797 GT:DR:DV 0/0:104954:11 +chr20 4685581 13 AACTAGGAGAC N . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4685610;STD_quant_start=4.358899;STD_quant_stop=8.717798;Kurtosis_quant_start=-1.310774;Kurtosis_quant_stop=-1.857551;SVTYPE=DEL;SUPTYPE=AL;SVLEN=-29;STRANDS=+-;STRANDS2=9,8,9,8;RE=17;REF_strand=68454,36564;Strandbias_pval=0.31361;AF=0.000161877 GT:DR:DV 0/0:105001:17 +chr20 4685646 14 N GATGCAGCATATATATAAGTAAAAGAAAGCCCAAAGGACAGTGATG . PASS IMPRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4685653;STD_quant_start=10.449880;STD_quant_stop=6.488451;Kurtosis_quant_start=-0.300360;Kurtosis_quant_stop=-0.456624;SVTYPE=INS;SUPTYPE=AL;SVLEN=15;STRANDS=+-;STRANDS2=11,5,11,5;RE=16;REF_strand=68454,36654;Strandbias_pval=1;AF=0.000152224 GT:DR:DV 0/0:105092:16 +chr20 4685709 15 TAAATCCTGTCCTTCT N . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4685726;STD_quant_start=4.868265;STD_quant_stop=2.509980;Kurtosis_quant_start=-0.238829;Kurtosis_quant_stop=-1.717687;SVTYPE=DEL;SUPTYPE=AL;SVLEN=-17;STRANDS=+-;STRANDS2=13,8,13,8;RE=21;REF_strand=68456,36777;Strandbias_pval=0.820052;AF=0.000199557 GT:DR:DV 0/0:105212:21 +chr20 4685765 16 GCAAGAACACA N . PASS IMPRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4685786;STD_quant_start=10.063134;STD_quant_stop=8.992590;Kurtosis_quant_start=-1.927149;Kurtosis_quant_stop=-1.983584;SVTYPE=DEL;SUPTYPE=AL,NR;SVLEN=-21;STRANDS=+-;STRANDS2=17,13,17,13;RE=30;REF_strand=68456,36865;Strandbias_pval=0.343553;AF=0.000284843 GT:DR:DV 0/0:105291:30 +chr20 4685835 17 N TTTCTTTTTTTT . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4685835;STD_quant_start=0.000000;STD_quant_stop=1.949359;Kurtosis_quant_start=-0.911089;Kurtosis_quant_stop=-1.179252;SVTYPE=INS;SUPTYPE=AL;SVLEN=12;STRANDS=+-;STRANDS2=15,5,15,5;RE=20;REF_strand=68456,36956;Strandbias_pval=0.483007;AF=0.000189732 GT:DR:DV 0/0:105392:20 +chr20 4685863 18 N TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT . PASS IMPRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4685863;STD_quant_start=7.835815;STD_quant_stop=11.331372;Kurtosis_quant_start=-0.651577;Kurtosis_quant_stop=0.264612;SVTYPE=INS;SUPTYPE=AL;SVLEN=21;STRANDS=+-;STRANDS2=11,2,11,2;RE=13;REF_strand=68458,37000;Strandbias_pval=0.158841;AF=0.000123272 GT:DR:DV 0/0:105445:13 +chr20 4685835 19 TTTTTAAACGGAGCGCA N . PASS IMPRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4685859;STD_quant_start=7.257180;STD_quant_stop=11.453841;Kurtosis_quant_start=-1.879656;Kurtosis_quant_stop=-1.557284;SVTYPE=DEL;SUPTYPE=AL;SVLEN=-24;STRANDS=+-;STRANDS2=32,11,32,11;RE=43;REF_strand=68456,36973;Strandbias_pval=0.205646;AF=0.000407857 GT:DR:DV 0/0:105386:43 +chr20 4685929 20 GTGATGGTCAGT N . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4685946;STD_quant_start=7.853497;STD_quant_stop=7.628470;Kurtosis_quant_start=-1.827182;Kurtosis_quant_stop=-1.848657;SVTYPE=DEL;SUPTYPE=AL;SVLEN=-17;STRANDS=+-;STRANDS2=38,24,38,24;RE=62;REF_strand=68451,37099;Strandbias_pval=0.595102;AF=0.000587399 GT:DR:DV 0/0:105488:62 +chr20 4685990 21 AAATATTAATCTCA N . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4686007;STD_quant_start=9.143304;STD_quant_stop=8.012490;Kurtosis_quant_start=-1.915456;Kurtosis_quant_stop=-1.384643;SVTYPE=DEL;SUPTYPE=AL;SVLEN=-17;STRANDS=+-;STRANDS2=11,6,11,6;RE=17;REF_strand=68231,37212;Strandbias_pval=1;AF=0.000161225 GT:DR:DV 0/0:105426:17 +chr20 4686090 22 N TTTTTTTTTTTTTTTTT . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4686096;STD_quant_start=8.882567;STD_quant_stop=6.715653;Kurtosis_quant_start=-1.648575;Kurtosis_quant_stop=-1.463973;SVTYPE=INS;SUPTYPE=AL;SVLEN=11;STRANDS=+-;STRANDS2=14,3,14,3;RE=17;REF_strand=67751,37380;Strandbias_pval=0.137332;AF=0.000161703 GT:DR:DV 0/0:105114:17 +chr20 4686116 23 GGGGAGCTGGAGCTTT N . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4686137;STD_quant_start=6.236986;STD_quant_stop=9.322017;Kurtosis_quant_start=-1.547467;Kurtosis_quant_stop=-1.949331;SVTYPE=DEL;SUPTYPE=AL;SVLEN=-21;STRANDS=+-;STRANDS2=11,8,11,8;RE=19;REF_strand=67622,37420;Strandbias_pval=0.633239;AF=0.00018088 GT:DR:DV 0/0:105023:19 +chr20 4686154 24 N AAAAAAAGAAAGAGAA . PASS IMPRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4686162;STD_quant_start=11.018923;STD_quant_stop=9.895285;Kurtosis_quant_start=-1.952371;Kurtosis_quant_stop=-2.049971;SVTYPE=INS;SUPTYPE=AL;SVLEN=12;STRANDS=+-;STRANDS2=17,7,17,7;RE=24;REF_strand=67463,37469;Strandbias_pval=0.670745;AF=0.00022872 GT:DR:DV 0/0:104908:24 +chr20 4686249 25 N TTTTTTTTTTTTTTTTTTTTTTT . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4686250;STD_quant_start=0.948683;STD_quant_stop=2.258318;Kurtosis_quant_start=0.051434;Kurtosis_quant_stop=-0.941308;SVTYPE=INS;SUPTYPE=AL;SVLEN=11;STRANDS=+-;STRANDS2=16,4,16,4;RE=20;REF_strand=66943,37649;Strandbias_pval=0.165569;AF=0.000191219 GT:DR:DV 0/0:104572:20 +chr20 4686414 26 N GCACGCACACACACGCACACGCACACACACACACG . PASS IMPRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4686426;STD_quant_start=10.564090;STD_quant_stop=7.930952;Kurtosis_quant_start=-1.453216;Kurtosis_quant_stop=-1.051817;SVTYPE=INS;SUPTYPE=AL;SVLEN=12;STRANDS=+-;STRANDS2=12,5,12,5;RE=17;REF_strand=65819,37979;Strandbias_pval=0.62259;AF=0.00016378 GT:DR:DV 0/0:103781:17 +chr20 4686550 27 AGCCGCGGGGGC N . STRANDBIAS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4686566;STD_quant_start=4.888032;STD_quant_stop=5.035588;Kurtosis_quant_start=-1.312828;Kurtosis_quant_stop=-0.404178;SVTYPE=DEL;SUPTYPE=AL,NR;SVLEN=-16;STRANDS=+-;STRANDS2=48,8,48,8;RE=56;REF_strand=64925,38251;Strandbias_pval=0.000250795;AF=0.000542762 GT:DR:DV 0/0:103120:56 +chr20 4686560 28 GGACCCCGGGC N . STRANDBIAS IMPRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4686613;STD_quant_start=17.496218;STD_quant_stop=5.179144;Kurtosis_quant_start=-2.210741;Kurtosis_quant_stop=-1.402743;SVTYPE=DEL;SUPTYPE=AL,NR;SVLEN=-53;STRANDS=+-;STRANDS2=12,23,12,23;RE=35;REF_strand=64826,38335;Strandbias_pval=0.000708429;AF=0.000339276 GT:DR:DV 0/0:103126:35 +chr20 4686637 29 GGAGGGGCCGGG N . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4686648;STD_quant_start=5.194188;STD_quant_stop=6.044056;Kurtosis_quant_start=-1.724945;Kurtosis_quant_stop=-1.639620;SVTYPE=DEL;SUPTYPE=AL;SVLEN=-11;STRANDS=+-;STRANDS2=49,49,49,49;RE=98;REF_strand=64665,38550;Strandbias_pval=0.0118685;AF=0.000949474 GT:DR:DV 0/0:103117:98 +chr20 4686720 30 TGGCTTCGCTTTTCAGGTTAGGAAAGCTCCCTTTACTGCGCGTTGGGGGGCTGGGGGAG N . STRANDBIAS IMPRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4686779;STD_quant_start=13.855375;STD_quant_stop=12.853015;Kurtosis_quant_start=-2.011984;Kurtosis_quant_stop=-1.892342;SVTYPE=DEL;SUPTYPE=AL,NR;SVLEN=-59;STRANDS=+-;STRANDS2=33,38,33,38;RE=71;REF_strand=64235,38796;Strandbias_pval=0.00687956;AF=0.000689113 GT:DR:DV 0/0:102960:71 +chr20 4686777 31 CGGAGCCCCGTTA N . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4686800;STD_quant_start=6.496153;STD_quant_stop=6.580274;Kurtosis_quant_start=-0.061919;Kurtosis_quant_stop=1.565777;SVTYPE=DEL;SUPTYPE=AL;SVLEN=-23;STRANDS=+-;STRANDS2=4,8,4,8;RE=12;REF_strand=64092,38885;Strandbias_pval=0.0686345;AF=0.000116531 GT:DR:DV 0/0:102965:12 +chr20 4686928 32 AGGGGCGCCTGGGGGC N . STRANDBIAS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4686943;STD_quant_start=7.281966;STD_quant_stop=8.104887;Kurtosis_quant_start=-1.273445;Kurtosis_quant_stop=-1.466445;SVTYPE=DEL;SUPTYPE=AL,NR;SVLEN=-15;STRANDS=+-;STRANDS2=63,86,63,86;RE=149;REF_strand=63393,39230;Strandbias_pval=1.75404e-06;AF=0.00145192 GT:DR:DV 0/0:102474:149 +chr20 4686963 33 N CCGCGTTCGTTCCCCACCA . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4686969;STD_quant_start=9.496411;STD_quant_stop=6.829082;Kurtosis_quant_start=-2.009117;Kurtosis_quant_stop=-1.775634;SVTYPE=INS;SUPTYPE=AL;SVLEN=11;STRANDS=+-;STRANDS2=18,4,18,4;RE=22;REF_strand=63217,39337;Strandbias_pval=0.0767019;AF=0.000214521 GT:DR:DV 0/0:102532:22 +chr20 4686997 34 GCCCAGAACGCCCCTTGGCAAGGCCTGGCGCTTCCGCGATGCCCAGAGGGTGCTT N . PASS IMPRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4687054;STD_quant_start=16.398171;STD_quant_stop=13.820275;Kurtosis_quant_start=-2.043564;Kurtosis_quant_stop=-1.995434;SVTYPE=DEL;SUPTYPE=AL;SVLEN=-57;STRANDS=+-;STRANDS2=39,42,39,42;RE=81;REF_strand=63048,39458;Strandbias_pval=0.0161272;AF=0.000790198 GT:DR:DV 0/0:102425:81 +chr20 4687051 35 N GGGGGGGGGGG . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4687052;STD_quant_start=3.860052;STD_quant_stop=4.949747;Kurtosis_quant_start=0.326930;Kurtosis_quant_stop=-0.960831;SVTYPE=INS;SUPTYPE=AL;SVLEN=11;STRANDS=+-;STRANDS2=13,2,13,2;RE=15;REF_strand=62977,39519;Strandbias_pval=0.0606088;AF=0.000146347 GT:DR:DV 0/0:102481:15 +chr20 4687318 36 N GCCGCTGCGTG . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4687329;STD_quant_start=8.414274;STD_quant_stop=5.839521;Kurtosis_quant_start=-0.951488;Kurtosis_quant_stop=0.131867;SVTYPE=INS;SUPTYPE=AL;SVLEN=11;STRANDS=+-;STRANDS2=7,6,7,6;RE=13;REF_strand=61948,39742;Strandbias_pval=0.584715;AF=0.00012784 GT:DR:DV 0/0:101677:13 +chr20 4687332 37 AGGTCTGCGGCCTGGCCCCAGGT N . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4687355;STD_quant_start=5.347897;STD_quant_stop=5.385165;Kurtosis_quant_start=-1.708832;Kurtosis_quant_stop=-1.766165;SVTYPE=DEL;SUPTYPE=AL;SVLEN=-23;STRANDS=+-;STRANDS2=9,10,9,10;RE=19;REF_strand=61892,39742;Strandbias_pval=0.245645;AF=0.000186945 GT:DR:DV 0/0:101615:19 +chr20 4687374 38 CCTCCCAGTCC N . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4687393;STD_quant_start=9.441550;STD_quant_stop=7.916228;Kurtosis_quant_start=-0.790394;Kurtosis_quant_stop=-0.953223;SVTYPE=DEL;SUPTYPE=AL;SVLEN=-19;STRANDS=+-;STRANDS2=31,11,31,11;RE=42;REF_strand=61742,39742;Strandbias_pval=0.112699;AF=0.000413858 GT:DR:DV 0/0:101442:42 +chr20 4687387 39 N GGCTGAAGAGAT . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4687390;STD_quant_start=3.714835;STD_quant_stop=4.647580;Kurtosis_quant_start=1.711854;Kurtosis_quant_stop=-0.883391;SVTYPE=INS;SUPTYPE=AL;SVLEN=11;STRANDS=+-;STRANDS2=12,2,12,2;RE=14;REF_strand=61724,39742;Strandbias_pval=0.0602252;AF=0.000137977 GT:DR:DV 0/0:101452:14 +chr20 4687424 40 CAACCAGCCTCGGAT N . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4687448;STD_quant_start=8.717798;STD_quant_stop=9.593748;Kurtosis_quant_start=-1.709530;Kurtosis_quant_stop=-1.528945;SVTYPE=DEL;SUPTYPE=AL;SVLEN=-24;STRANDS=+-;STRANDS2=37,14,37,14;RE=51;REF_strand=61611,39742;Strandbias_pval=0.113546;AF=0.000503192 GT:DR:DV 0/0:101302:51 +chr20 4687590 41 N TTTTTTTTTTT . STRANDBIAS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4687590;STD_quant_start=0.000000;STD_quant_stop=0.987421;Kurtosis_quant_start=3.084413;Kurtosis_quant_stop=0.560347;SVTYPE=INS;SUPTYPE=AL;SVLEN=12;STRANDS=+-;STRANDS2=79,2,79,2;RE=81;REF_strand=61090,39742;Strandbias_pval=4.84712e-15;AF=0.000803316 GT:DR:DV 0/0:100751:81 +chr20 4687590 42 TTTTTTTTTTAACCTCG N . STRANDBIAS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4687608;STD_quant_start=4.238106;STD_quant_stop=7.567644;Kurtosis_quant_start=-1.426765;Kurtosis_quant_stop=-1.709963;SVTYPE=DEL;SUPTYPE=AL,NR;SVLEN=-18;STRANDS=+-;STRANDS2=22,30,22,30;RE=52;REF_strand=61074,39742;Strandbias_pval=0.00993645;AF=0.000515791 GT:DR:DV 0/0:100764:52 +chr20 4687648 43 AGCTCTCCGTTTTT N . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4687665;STD_quant_start=4.940826;STD_quant_stop=5.965588;Kurtosis_quant_start=-1.653854;Kurtosis_quant_stop=-1.685298;SVTYPE=DEL;SUPTYPE=AL;SVLEN=-17;STRANDS=+-;STRANDS2=16,19,16,19;RE=35;REF_strand=60918,39742;Strandbias_pval=0.0839827;AF=0.000347705 GT:DR:DV 0/0:100625:35 +chr20 4687668 44 N TTTTTTTTTTTTTTTTTTTTTTTTTTG . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4687675;STD_quant_start=7.334848;STD_quant_stop=7.791020;Kurtosis_quant_start=-0.630899;Kurtosis_quant_stop=0.091411;SVTYPE=INS;SUPTYPE=AL;SVLEN=13;STRANDS=+-;STRANDS2=11,3,11,3;RE=14;REF_strand=60875,39742;Strandbias_pval=0.273325;AF=0.000139141 GT:DR:DV 0/0:100603:14 +chr20 4687704 45 CAGTTTCACTGCTGTAATGATGAGGATCTT N . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4687727;STD_quant_start=8.492644;STD_quant_stop=9.410765;Kurtosis_quant_start=-0.955820;Kurtosis_quant_stop=-2.112883;SVTYPE=DEL;SUPTYPE=AL,NR;SVLEN=-23;STRANDS=+-;STRANDS2=18,14,18,14;RE=32;REF_strand=60756,39742;Strandbias_pval=0.718213;AF=0.000318414 GT:DR:DV 0/0:100466:32 +chr20 4687726 46 TCTTCATGGCCGCGTTATTT N . PASS IMPRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4687786;STD_quant_start=18.465144;STD_quant_stop=13.079638;Kurtosis_quant_start=-2.057741;Kurtosis_quant_stop=-2.082674;SVTYPE=DEL;SUPTYPE=AL;SVLEN=-60;STRANDS=+-;STRANDS2=30,23,30,23;RE=53;REF_strand=60614,39741;Strandbias_pval=0.57685;AF=0.000528125 GT:DR:DV 0/0:100302:53 +chr20 4687924 47 N TTTCATATTCATTATAAGTGGCGTGTGTATTAGC . PASS IMPRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4687934;STD_quant_start=15.346009;STD_quant_stop=12.529964;Kurtosis_quant_start=-1.723511;Kurtosis_quant_stop=-1.023053;SVTYPE=INS;SUPTYPE=AL;SVLEN=20;STRANDS=+-;STRANDS2=7,6,7,6;RE=13;REF_strand=60120,39736;Strandbias_pval=0.778276;AF=0.000130187 GT:DR:DV 0/0:99843:13 +chr20 4688011 48 N AAAAAAAAAAAAAAAAAAA . STRANDBIAS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4688014;STD_quant_start=0.000000;STD_quant_stop=2.121320;Kurtosis_quant_start=0.646993;Kurtosis_quant_stop=-0.498215;SVTYPE=INS;SUPTYPE=AL;SVLEN=11;STRANDS=+-;STRANDS2=2,16,2,16;RE=18;REF_strand=59485,39603;Strandbias_pval=2.53195e-05;AF=0.000181657 GT:DR:DV 0/0:99070:18 +chr20 4688000 49 N . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4688013;STD_quant_start=5.495453;STD_quant_stop=5.272571;Kurtosis_quant_start=-1.394667;Kurtosis_quant_stop=-1.556086;SVTYPE=DEL;SUPTYPE=AL;SVLEN=-13;STRANDS=+-;STRANDS2=7,9,7,9;RE=16;REF_strand=59607,39644;Strandbias_pval=0.206912;AF=0.000161207 GT:DR:DV 0/0:99235:16 diff --git a/SVs_sniffles/vcf/58648_bodySnif.vcf b/SVs_sniffles/vcf/58648_bodySnif.vcf new file mode 100644 index 0000000..ef26c13 --- /dev/null +++ b/SVs_sniffles/vcf/58648_bodySnif.vcf @@ -0,0 +1,38 @@ +##fileformat=VCFv4.1 +##source=Sniffles +##fileDate=20210810:59:16 AMef_minus +##contig= +##ALT= +##ALT= +##ALT= +##ALT= +##ALT= +##ALT= +##FILTER= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##FORMAT= +##FORMAT= +##FORMAT= +#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT bamfilt/58648_f.bam +chr20 4699380 0 N GGTGGTGGCTGGGGGGCAGCCTCATGGTGGTGGCTGGGGGCAGCCTCATGGTGGTGGCTGGGGGCAGCCTCATGGTGGTGGCTGGGGGCAGCCCCATGGTGGTGGCTGGGGACAGCCTCATGGTGGTGGCTGGGGGCAGCCCCAT . STRANDBIAS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4699380;STD_quant_start=0.000000;STD_quant_stop=1.791647;Kurtosis_quant_start=-0.224687;Kurtosis_quant_stop=0.069757;SVTYPE=INS;SUPTYPE=AL;SVLEN=144;STRANDS=+-;STRANDS2=735,665,735,665;RE=1400;REF_strand=5590,5972;Strandbias_pval=0.00354045;AF=0.121086 GT:DR:DV 0/0:10162:1400 +chr20 4699439 1 N GGGGCAGCCTCATGGTGGTGGCTGGGGCAGCCCCATGGTGGTGGCTGGGGACAGCCTCATGGTGGTGGCTGGGGGCAGCCCCATGGTGGTGGCTGGGGCAGCCTCATGGTGGTGGCTGGGGGGCAGCCTCATGGTGGTGGCT . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4699439;STD_quant_start=6.195154;STD_quant_stop=5.866648;Kurtosis_quant_start=-1.430978;Kurtosis_quant_stop=-1.266272;SVTYPE=INS;SUPTYPE=AL;SVLEN=143;STRANDS=+-;STRANDS2=531,586,531,586;RE=1117;REF_strand=5590,5972;Strandbias_pval=0.615997;AF=0.0966096 GT:DR:DV 0/0:10445:1117 diff --git a/SVs_sniffles/vcf/58648_promoterSnif.vcf b/SVs_sniffles/vcf/58648_promoterSnif.vcf new file mode 100644 index 0000000..ac47225 --- /dev/null +++ b/SVs_sniffles/vcf/58648_promoterSnif.vcf @@ -0,0 +1,106 @@ +##fileformat=VCFv4.1 +##source=Sniffles +##fileDate=20210811:55:42 AMef_minus +##contig= +##ALT= +##ALT= +##ALT= +##ALT= +##ALT= +##ALT= +##FILTER= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##FORMAT= +##FORMAT= +##FORMAT= +#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT promoterbamfilt/58648_f.bam +chr20 4685162 0 GATTGGTCCTGA N . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4685180;STD_quant_start=5.075895;STD_quant_stop=3.670230;Kurtosis_quant_start=-1.770413;Kurtosis_quant_stop=-1.120232;SVTYPE=DEL;SUPTYPE=AL,NR;SVLEN=-18;STRANDS=+-;STRANDS2=19,15,19,15;RE=34;REF_strand=119375,138331;Strandbias_pval=0.303526;AF=0.000131933 GT:DR:DV 0/0:257672:34 +chr20 4685147 1 N CCCCCCCCCCC . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4685160;STD_quant_start=6.016644;STD_quant_stop=9.792855;Kurtosis_quant_start=-1.784462;Kurtosis_quant_stop=-1.565044;SVTYPE=INS;SUPTYPE=AL;SVLEN=11;STRANDS=+-;STRANDS2=5,13,5,13;RE=18;REF_strand=119358,138142;Strandbias_pval=0.155603;AF=6.99029e-05 GT:DR:DV 0/0:257482:18 +chr20 4685224 2 N TTTTTTTTTTT . STRANDBIAS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4685224;STD_quant_start=0.000000;STD_quant_stop=1.539449;Kurtosis_quant_start=46.483508;Kurtosis_quant_stop=0.851645;SVTYPE=INS;SUPTYPE=AL;SVLEN=11;STRANDS=+-;STRANDS2=7908,187,7908,187;RE=8095;REF_strand=119402,139002;Strandbias_pval=0;AF=0.0313269 GT:DR:DV 0/0:250309:8095 +chr20 4685224 3 TTTTTTTTTTTT N . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4685235;STD_quant_start=0.000000;STD_quant_stop=1.147236;Kurtosis_quant_start=2.560888;Kurtosis_quant_stop=1.917294;SVTYPE=DEL;SUPTYPE=AL,NR;SVLEN=-11;STRANDS=+-;STRANDS2=510,655,510,655;RE=1165;REF_strand=119405,139077;Strandbias_pval=0.099192;AF=0.00450708 GT:DR:DV 0/0:257317:1165 +chr20 4685224 4 N TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT . PASS IMPRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4685224;STD_quant_start=21.477896;STD_quant_stop=11.734564;Kurtosis_quant_start=0.012672;Kurtosis_quant_stop=4.950709;SVTYPE=INS;SUPTYPE=AL;SVLEN=65;STRANDS=+-;STRANDS2=7,3,7,3;RE=10;REF_strand=119402,139002;Strandbias_pval=0.203492;AF=3.86991e-05 GT:DR:DV 0/0:258394:10 +chr20 4685224 5 CCTCAGCTTTTTTTTTTTTTTTTGTAAAGAGACAAAGAGTGAGACAGGGTCTTGGCCTATAGCCCTGTGGCCCAGGCTGGAGTGCAGTGGCACAATTAAAGCTCACTGCAGCCTCTACCTCCTGGGCTCAAGCAA N . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4685337;STD_quant_start=0.316228;STD_quant_stop=8.354639;Kurtosis_quant_start=0.528219;Kurtosis_quant_stop=-1.296068;SVTYPE=DEL;SUPTYPE=AL,NR;SVLEN=-113;STRANDS=+-;STRANDS2=11,5,11,5;RE=16;REF_strand=119437,139818;Strandbias_pval=0.0811756;AF=6.17153e-05 GT:DR:DV 0/0:259239:16 +chr20 4685314 6 AAAGCTCACTGCAGC N . STRANDBIAS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4685325;STD_quant_start=2.085144;STD_quant_stop=2.032347;Kurtosis_quant_start=3.173901;Kurtosis_quant_stop=0.535932;SVTYPE=DEL;SUPTYPE=AL,NR;SVLEN=-11;STRANDS=+-;STRANDS2=36,11,36,11;RE=47;REF_strand=119467,140421;Strandbias_pval=2.54663e-05;AF=0.000180847 GT:DR:DV 0/0:259841:47 +chr20 4685341 7 N AATCTCCTGCTGTCTTGAT . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4685347;STD_quant_start=6.361342;STD_quant_stop=9.615959;Kurtosis_quant_start=-1.961407;Kurtosis_quant_stop=-1.702875;SVTYPE=INS;SUPTYPE=AL;SVLEN=13;STRANDS=+-;STRANDS2=18,13,18,13;RE=31;REF_strand=119472,140721;Strandbias_pval=0.207756;AF=0.000119142 GT:DR:DV 0/0:260162:31 +chr20 4685413 8 N TTTTTTTATTTTTTTTTTTTTTTTTT . STRANDBIAS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4685413;STD_quant_start=0.000000;STD_quant_stop=3.956283;Kurtosis_quant_start=1.117974;Kurtosis_quant_stop=-0.912073;SVTYPE=INS;SUPTYPE=AL;SVLEN=11;STRANDS=+-;STRANDS2=194,36,194,36;RE=230;REF_strand=119480,141404;Strandbias_pval=1.39757e-33;AF=0.000881618 GT:DR:DV 0/0:260654:230 +chr20 4685439 9 N CTGGCCACCCCAGGCT . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4685440;STD_quant_start=4.847680;STD_quant_stop=4.949747;Kurtosis_quant_start=-1.699731;Kurtosis_quant_stop=-1.556969;SVTYPE=INS;SUPTYPE=AL;SVLEN=13;STRANDS=+-;STRANDS2=8,13,8,13;RE=21;REF_strand=119480,141757;Strandbias_pval=0.51952;AF=8.03868e-05 GT:DR:DV 0/0:261216:21 +chr20 4685507 10 N ACAAAAAAAAAAAAAAAAAAAAAAAA . PASS IMPRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4685520;STD_quant_start=13.374416;STD_quant_stop=11.146748;Kurtosis_quant_start=-2.223900;Kurtosis_quant_stop=-2.053521;SVTYPE=INS;SUPTYPE=AL;SVLEN=11;STRANDS=+-;STRANDS2=17,16,17,16;RE=33;REF_strand=119482,142489;Strandbias_pval=0.600757;AF=0.000125968 GT:DR:DV 0/0:261938:33 +chr20 4685522 11 CAGGCCTGAGCCACTG N . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4685537;STD_quant_start=2.645751;STD_quant_stop=2.980707;Kurtosis_quant_start=-0.697809;Kurtosis_quant_stop=-1.400228;SVTYPE=DEL;SUPTYPE=AL,NR;SVLEN=-15;STRANDS=+-;STRANDS2=29,24,29,24;RE=53;REF_strand=119482,142652;Strandbias_pval=0.214444;AF=0.000202187 GT:DR:DV 0/0:262081:53 +chr20 4685554 12 AACATTCTTAAATCTCTTTCCTTACATGCTTCCTAAA N . STRANDBIAS IMPRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4685591;STD_quant_start=13.071310;STD_quant_stop=12.508026;Kurtosis_quant_start=-1.791432;Kurtosis_quant_stop=-1.871758;SVTYPE=DEL;SUPTYPE=AL;SVLEN=-37;STRANDS=+-;STRANDS2=83,59,83,59;RE=142;REF_strand=119482,143121;Strandbias_pval=0.00230966;AF=0.00054074 GT:DR:DV 0/0:262461:142 +chr20 4685613 13 CAGGGCATGCCTGGTTTACGCCCATTTCACTTTAAAAGTGCCCAATTTG N . PASS IMPRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4685677;STD_quant_start=15.658863;STD_quant_stop=11.211601;Kurtosis_quant_start=0.537488;Kurtosis_quant_stop=-0.574761;SVTYPE=DEL;SUPTYPE=AL,NR;SVLEN=-64;STRANDS=+-;STRANDS2=6,5,6,5;RE=11;REF_strand=119482,143808;Strandbias_pval=0.560939;AF=4.1779e-05 GT:DR:DV 0/0:263279:11 +chr20 4685671 14 ATCCCCCTCCCTCTAA N . PASS IMPRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4685709;STD_quant_start=10.122329;STD_quant_stop=6.605165;Kurtosis_quant_start=-2.068403;Kurtosis_quant_stop=-1.540796;SVTYPE=DEL;SUPTYPE=AL;SVLEN=-38;STRANDS=+-;STRANDS2=67,89,67,89;RE=156;REF_strand=119482,144306;Strandbias_pval=0.574222;AF=0.000591384 GT:DR:DV 0/0:263632:156 +chr20 4685697 15 TCTAAATCCTG N . PASS IMPRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4685732;STD_quant_start=7.778175;STD_quant_stop=19.370080;Kurtosis_quant_start=0.117296;Kurtosis_quant_stop=-1.492332;SVTYPE=DEL;SUPTYPE=AL,NR;SVLEN=-35;STRANDS=+-;STRANDS2=7,7,7,7;RE=14;REF_strand=119482,144547;Strandbias_pval=0.791872;AF=5.30245e-05 GT:DR:DV 0/0:264015:14 +chr20 4685695 16 N CTTTCTCTTCTTT . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4685718;STD_quant_start=9.677141;STD_quant_stop=8.957416;Kurtosis_quant_start=-2.117477;Kurtosis_quant_stop=-1.868048;SVTYPE=INS;SUPTYPE=AL;SVLEN=12;STRANDS=+-;STRANDS2=16,19,16,19;RE=35;REF_strand=119482,144477;Strandbias_pval=1;AF=0.000132596 GT:DR:DV 0/0:263924:35 +chr20 4685797 17 TTTCATAGAAGATATCTCAGGTAATGTGCAAACACGGGTTTTTA N . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4685826;STD_quant_start=1.643168;STD_quant_stop=7.930952;Kurtosis_quant_start=-0.515215;Kurtosis_quant_stop=-1.591496;SVTYPE=DEL;SUPTYPE=AL,NR;SVLEN=-29;STRANDS=+-;STRANDS2=7,10,7,10;RE=17;REF_strand=119484,145351;Strandbias_pval=0.811437;AF=6.41909e-05 GT:DR:DV 0/0:264818:17 +chr20 4685876 18 CACCTAAATCAT N . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4685887;STD_quant_start=4.598136;STD_quant_stop=5.126960;Kurtosis_quant_start=-1.871274;Kurtosis_quant_stop=-0.386622;SVTYPE=DEL;SUPTYPE=AL,NR;SVLEN=-11;STRANDS=+-;STRANDS2=19,23,19,23;RE=42;REF_strand=119482,145999;Strandbias_pval=1;AF=0.000158203 GT:DR:DV 0/0:265439:42 +chr20 4685930 19 N AAGGTGTGGTGGTA . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4685936;STD_quant_start=9.577935;STD_quant_stop=8.335088;Kurtosis_quant_start=-2.183793;Kurtosis_quant_stop=-2.101685;SVTYPE=INS;SUPTYPE=AL;SVLEN=12;STRANDS=+-;STRANDS2=22,17,22,17;RE=39;REF_strand=119461,146404;Strandbias_pval=0.197175;AF=0.000146691 GT:DR:DV 0/0:265826:39 +chr20 4685991 20 N AAACAATGGTA . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4685997;STD_quant_start=8.506963;STD_quant_stop=7.458658;Kurtosis_quant_start=-2.018854;Kurtosis_quant_stop=-1.973109;SVTYPE=INS;SUPTYPE=AL;SVLEN=12;STRANDS=+-;STRANDS2=18,20,18,20;RE=38;REF_strand=119186,147025;Strandbias_pval=0.747454;AF=0.000142744 GT:DR:DV 0/0:266173:38 +chr20 4686021 21 TTTTGCTCTCC N . STRANDBIAS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4686034;STD_quant_start=6.668155;STD_quant_stop=6.560161;Kurtosis_quant_start=-1.154844;Kurtosis_quant_stop=-1.982147;SVTYPE=DEL;SUPTYPE=AL;SVLEN=-13;STRANDS=+-;STRANDS2=31,81,31,81;RE=112;REF_strand=118884,147357;Strandbias_pval=0.000272931;AF=0.000420671 GT:DR:DV 0/0:266129:112 +chr20 4686075 22 CCTCATTCCTGAG N . STRANDBIAS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4686088;STD_quant_start=1.912562;STD_quant_stop=2.194491;Kurtosis_quant_start=0.431277;Kurtosis_quant_stop=0.977489;SVTYPE=DEL;SUPTYPE=AL;SVLEN=-13;STRANDS=+-;STRANDS2=73,4,73,4;RE=77;REF_strand=118491,147811;Strandbias_pval=2.88042e-21;AF=0.000289145 GT:DR:DV 0/0:266225:77 +chr20 4686075 23 CTCATTCCTGAGCCTTTCATTTT N . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4686099;STD_quant_start=4.543903;STD_quant_stop=3.589199;Kurtosis_quant_start=-1.484486;Kurtosis_quant_stop=-1.356438;SVTYPE=DEL;SUPTYPE=AL;SVLEN=-24;STRANDS=+-;STRANDS2=12,23,12,23;RE=35;REF_strand=118458,147860;Strandbias_pval=0.239097;AF=0.000131422 GT:DR:DV 0/0:266283:35 +chr20 4686158 24 GATGATTTTTACAGTCAATGAGCCACGTCAGG N . STRANDBIAS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4686190;STD_quant_start=6.426508;STD_quant_stop=3.794733;Kurtosis_quant_start=-1.101234;Kurtosis_quant_stop=-0.776747;SVTYPE=DEL;SUPTYPE=AL;SVLEN=-32;STRANDS=+-;STRANDS2=2,15,2,15;RE=17;REF_strand=117787,148498;Strandbias_pval=0.0064029;AF=6.38414e-05 GT:DR:DV 0/0:266268:17 +chr20 4686162 25 N TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT . PASS IMPRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4686203;STD_quant_start=14.943483;STD_quant_stop=6.450999;Kurtosis_quant_start=-2.004081;Kurtosis_quant_stop=-2.091464;SVTYPE=INS;SUPTYPE=AL;SVLEN=12;STRANDS=+-;STRANDS2=18,9,18,9;RE=27;REF_strand=117735,148573;Strandbias_pval=0.0205286;AF=0.000101386 GT:DR:DV 0/0:266281:27 +chr20 4686176 26 GGAGCGATGGCACCC N . PASS IMPRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4686203;STD_quant_start=11.060440;STD_quant_stop=6.918291;Kurtosis_quant_start=-1.926938;Kurtosis_quant_stop=-1.138420;SVTYPE=DEL;SUPTYPE=AL,NR;SVLEN=-27;STRANDS=+-;STRANDS2=46,57,46,57;RE=103;REF_strand=117682,148626;Strandbias_pval=0.921343;AF=0.00038677 GT:DR:DV 0/0:266205:103 +chr20 4686249 27 N TTTTTTTTTTT . STRANDBIAS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4686249;STD_quant_start=1.612452;STD_quant_stop=4.427189;Kurtosis_quant_start=-0.401875;Kurtosis_quant_stop=0.272999;SVTYPE=INS;SUPTYPE=AL;SVLEN=11;STRANDS=+-;STRANDS2=13,3,13,3;RE=16;REF_strand=117174,149142;Strandbias_pval=0.00397283;AF=6.0079e-05 GT:DR:DV 0/0:266300:16 +chr20 4686249 28 N TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4686281;STD_quant_start=6.774954;STD_quant_stop=9.648834;Kurtosis_quant_start=-1.803474;Kurtosis_quant_stop=-1.832902;SVTYPE=INS;SUPTYPE=AL;SVLEN=13;STRANDS=+-;STRANDS2=13,7,13,7;RE=20;REF_strand=117023,149280;Strandbias_pval=0.0712356;AF=7.51024e-05 GT:DR:DV 0/0:266283:20 +chr20 4686310 29 CGCCGCCGCTTCCCT N . STRANDBIAS IMPRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4686405;STD_quant_start=20.332750;STD_quant_stop=18.727832;Kurtosis_quant_start=-1.986674;Kurtosis_quant_stop=-1.975489;SVTYPE=DEL;SUPTYPE=AL;SVLEN=-95;STRANDS=+-;STRANDS2=83,246,83,246;RE=329;REF_strand=116211,150031;Strandbias_pval=6.50354e-12;AF=0.00123572 GT:DR:DV 0/0:265913:329 +chr20 4686362 30 TTGGTCCCCGCGCCGACCTCCGCCCGCGAGCGCCGCCGCTTCCCTTCCCCGCCCCGCGTCCCTCCCCCTCGGCCCCGCGCGTCGC N . PASS IMPRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4686445;STD_quant_start=5.585696;STD_quant_stop=18.072078;Kurtosis_quant_start=-0.501077;Kurtosis_quant_stop=-1.167793;SVTYPE=DEL;SUPTYPE=AL,NR;SVLEN=-83;STRANDS=+-;STRANDS2=7,6,7,6;RE=13;REF_strand=115855,150440;Strandbias_pval=0.578147;AF=4.8818e-05 GT:DR:DV 0/0:266282:13 +chr20 4686358 31 N CGCGGCGGCGTGGCCGG . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4686367;STD_quant_start=6.335087;STD_quant_stop=6.392704;Kurtosis_quant_start=-1.936911;Kurtosis_quant_stop=-1.642156;SVTYPE=INS;SUPTYPE=AL;SVLEN=11;STRANDS=+-;STRANDS2=14,17,14,17;RE=31;REF_strand=116187,150114;Strandbias_pval=0.858585;AF=0.00011641 GT:DR:DV 0/0:266270:31 +chr20 4686411 32 CGCGTCCCTCCCCCTCGGCCCCG N . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4686437;STD_quant_start=5.873355;STD_quant_stop=9.048020;Kurtosis_quant_start=-0.902318;Kurtosis_quant_stop=-1.649279;SVTYPE=DEL;SUPTYPE=AL,NR;SVLEN=-26;STRANDS=+-;STRANDS2=110,160,110,160;RE=270;REF_strand=115656,150575;Strandbias_pval=0.390131;AF=0.00101416 GT:DR:DV 0/0:265961:270 +chr20 4686486 33 CTTCTCCTCTC N . STRANDBIAS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4686497;STD_quant_start=1.426637;STD_quant_stop=1.541581;Kurtosis_quant_start=-0.816750;Kurtosis_quant_stop=-0.803250;SVTYPE=DEL;SUPTYPE=AL;SVLEN=-11;STRANDS=+-;STRANDS2=103,68,103,68;RE=171;REF_strand=115205,151129;Strandbias_pval=9.21612e-06;AF=0.000642051 GT:DR:DV 0/0:266163:171 +chr20 4686571 34 AGGACCCCGGGCC N . STRANDBIAS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4686585;STD_quant_start=2.028370;STD_quant_stop=2.408319;Kurtosis_quant_start=-0.216430;Kurtosis_quant_stop=0.053864;SVTYPE=DEL;SUPTYPE=AL;SVLEN=-14;STRANDS=+-;STRANDS2=44,26,44,26;RE=70;REF_strand=114656,151931;Strandbias_pval=0.000997983;AF=0.000262578 GT:DR:DV 0/0:266517:70 +chr20 4686569 35 CGGGTCCCAGGC N . PASS IMPRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4686662;STD_quant_start=10.526158;STD_quant_stop=16.988231;Kurtosis_quant_start=-1.880221;Kurtosis_quant_stop=-1.946259;SVTYPE=DEL;SUPTYPE=AL;SVLEN=-93;STRANDS=+-;STRANDS2=8,9,8,9;RE=17;REF_strand=114443,152309;Strandbias_pval=0.808382;AF=6.37296e-05 GT:DR:DV 0/0:266735:17 +chr20 4686588 36 N CCATACCTACT . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4686593;STD_quant_start=7.115125;STD_quant_stop=8.838835;Kurtosis_quant_start=-1.430770;Kurtosis_quant_stop=-1.979863;SVTYPE=INS;SUPTYPE=AL;SVLEN=11;STRANDS=+-;STRANDS2=11,22,11,22;RE=33;REF_strand=114594,152062;Strandbias_pval=0.295156;AF=0.000123755 GT:DR:DV 0/0:266623:33 +chr20 4686638 37 N GGGGGGGGGGGGGGGGG . PASS IMPRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4686643;STD_quant_start=9.757049;STD_quant_stop=12.271919;Kurtosis_quant_start=-0.287205;Kurtosis_quant_stop=-1.421777;SVTYPE=INS;SUPTYPE=AL;SVLEN=23;STRANDS=+-;STRANDS2=8,4,8,4;RE=12;REF_strand=114329,152542;Strandbias_pval=0.142308;AF=4.49655e-05 GT:DR:DV 0/0:266859:12 +chr20 4686637 38 GAGGGGCCGGGGGCT N . STRANDBIAS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4686653;STD_quant_start=4.793319;STD_quant_stop=5.195573;Kurtosis_quant_start=-1.641950;Kurtosis_quant_stop=-1.563669;SVTYPE=DEL;SUPTYPE=AL,NR;SVLEN=-16;STRANDS=+-;STRANDS2=96,237,96,237;RE=333;REF_strand=114296,152598;Strandbias_pval=1.60685e-07;AF=0.00124769 GT:DR:DV 0/0:266561:333 +chr20 4686670 39 GTCTCGGGCCT N . STRANDBIAS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4686684;STD_quant_start=2.962263;STD_quant_stop=2.932576;Kurtosis_quant_start=-0.456539;Kurtosis_quant_stop=0.979382;SVTYPE=DEL;SUPTYPE=AL;SVLEN=-14;STRANDS=+-;STRANDS2=50,30,50,30;RE=80;REF_strand=114099,152941;Strandbias_pval=0.000413369;AF=0.000299581 GT:DR:DV 0/0:266960:80 +chr20 4686720 40 TTGGCTTCGCTT N . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4686734;STD_quant_start=6.635466;STD_quant_stop=7.479383;Kurtosis_quant_start=-1.839622;Kurtosis_quant_stop=-1.662931;SVTYPE=DEL;SUPTYPE=AL;SVLEN=-14;STRANDS=+-;STRANDS2=56,80,56,80;RE=136;REF_strand=113799,153297;Strandbias_pval=0.794884;AF=0.00050918 GT:DR:DV 0/0:266960:136 +chr20 4686832 41 CCCCCTGCACCCCGCGCGGGTCCGGCCCAGCGGGCGATCGCTGGCGCCCAGGGAACTCCGGGAGGGCCGCCAGCGGGCTCCGCAGGGCGCGGGGCGGGGAGGGGCGCCTGGGGGCCGCGGGGCTCGCGCTCCCCGCCCGTTGGCCGCCCCTCGGAGGCCGAGATCGGGGCCC N . PASS IMPRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4686980;STD_quant_start=24.135037;STD_quant_stop=25.822471;Kurtosis_quant_start=-0.514145;Kurtosis_quant_stop=-1.475419;SVTYPE=DEL;SUPTYPE=AL,NR;SVLEN=-148;STRANDS=+-;STRANDS2=7,3,7,3;RE=10;REF_strand=112688,154962;Strandbias_pval=0.107101;AF=3.73622e-05 GT:DR:DV 0/0:267640:10 +chr20 4686853 42 CCCAGCGGGCGATCGC N . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4686870;STD_quant_start=2.406588;STD_quant_stop=3.915780;Kurtosis_quant_start=-0.301899;Kurtosis_quant_stop=-1.227742;SVTYPE=DEL;SUPTYPE=AL,NR;SVLEN=-17;STRANDS=+-;STRANDS2=19,30,19,30;RE=49;REF_strand=112938,154517;Strandbias_pval=0.666669;AF=0.000183208 GT:DR:DV 0/0:267406:49 +chr20 4686845 43 N CGCGGGGCCGGGCGACGGCCGCCAGGCA . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4686857;STD_quant_start=9.048481;STD_quant_stop=5.782517;Kurtosis_quant_start=-1.835132;Kurtosis_quant_stop=-1.723707;SVTYPE=INS;SUPTYPE=AL;SVLEN=13;STRANDS=+-;STRANDS2=14,19,14,19;RE=33;REF_strand=113012,154404;Strandbias_pval=1;AF=0.000123403 GT:DR:DV 0/0:267383:33 +chr20 4686903 44 CAGCGGGCTCCGCAGGGCGCGGGGCGGGGAGGGGCGCCTGGGGGCCGCGGGGCTCGCGCTCCCCGCCCGTTGGCCGCCCCTCGGAGGCCGAGATCGGGGCCCAGAACGCCCCTTGGCAAG N . STRANDBIAS IMPRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4687023;STD_quant_start=33.809762;STD_quant_stop=15.697133;Kurtosis_quant_start=-1.323163;Kurtosis_quant_stop=0.191661;SVTYPE=DEL;SUPTYPE=AL,NR;SVLEN=-120;STRANDS=+-;STRANDS2=9,1,9,1;RE=10;REF_strand=112340,155488;Strandbias_pval=0.00250225;AF=3.73374e-05 GT:DR:DV 0/0:267818:10 +chr20 4686968 45 N TGGCTGGCAAGC . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4686968;STD_quant_start=4.980916;STD_quant_stop=4.613644;Kurtosis_quant_start=-1.522771;Kurtosis_quant_stop=-1.451565;SVTYPE=INS;SUPTYPE=AL;SVLEN=12;STRANDS=+-;STRANDS2=26,17,26,17;RE=43;REF_strand=112284,155592;Strandbias_pval=0.0193529;AF=0.000160522 GT:DR:DV 0/0:267833:43 +chr20 4686997 46 CCCAGAACGCC N . STRANDBIAS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4687008;STD_quant_start=4.941322;STD_quant_stop=5.036533;Kurtosis_quant_start=-1.487839;Kurtosis_quant_stop=-1.061123;SVTYPE=DEL;SUPTYPE=AL;SVLEN=-11;STRANDS=+-;STRANDS2=66,55,66,55;RE=121;REF_strand=112126,155904;Strandbias_pval=0.00551542;AF=0.000451442 GT:DR:DV 0/0:267909:121 +chr20 4687066 47 GGGGCGCCCGCC N . STRANDBIAS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4687078;STD_quant_start=6.662352;STD_quant_stop=6.239765;Kurtosis_quant_start=-1.617879;Kurtosis_quant_stop=-1.262582;SVTYPE=DEL;SUPTYPE=AL;SVLEN=-12;STRANDS=+-;STRANDS2=103,296,103,296;RE=399;REF_strand=111693,156575;Strandbias_pval=5.36231e-11;AF=0.00148732 GT:DR:DV 0/0:267869:399 +chr20 4687049 48 N TTCTTTTTTTTT . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4687051;STD_quant_start=3.732100;STD_quant_stop=3.305839;Kurtosis_quant_start=-0.613523;Kurtosis_quant_stop=-0.540188;SVTYPE=INS;SUPTYPE=AL;SVLEN=11;STRANDS=+-;STRANDS2=10,18,10,18;RE=28;REF_strand=111849,156403;Strandbias_pval=0.570496;AF=0.000104379 GT:DR:DV 0/0:268224:28 +chr20 4687089 49 N TGGTAGAGGCAGCAGCACACA . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4687091;STD_quant_start=6.557439;STD_quant_stop=5.059644;Kurtosis_quant_start=-1.849889;Kurtosis_quant_stop=-1.388813;SVTYPE=INS;SUPTYPE=AL;SVLEN=19;STRANDS=+-;STRANDS2=8,12,8,12;RE=20;REF_strand=111582,156765;Strandbias_pval=1;AF=7.45304e-05 GT:DR:DV 0/0:268327:20 +chr20 4687128 50 CCCGGGAGGCGGCCCAGCCCTTCATCCTCGCCGCCTGAGCTTCTCC N . PASS IMPRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4687177;STD_quant_start=6.707327;STD_quant_stop=10.271033;Kurtosis_quant_start=-1.823498;Kurtosis_quant_stop=-1.976727;SVTYPE=DEL;SUPTYPE=AL;SVLEN=-49;STRANDS=+-;STRANDS2=86,85,86,85;RE=171;REF_strand=111213,157194;Strandbias_pval=0.0198421;AF=0.000637092 GT:DR:DV 0/0:268236:171 +chr20 4687145 51 N CCCCCCCCCCCC . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4687145;STD_quant_start=6.257303;STD_quant_stop=6.057418;Kurtosis_quant_start=-2.007548;Kurtosis_quant_stop=-2.046931;SVTYPE=INS;SUPTYPE=AL;SVLEN=12;STRANDS=+-;STRANDS2=13,14,13,14;RE=27;REF_strand=111294,157224;Strandbias_pval=0.558954;AF=0.000100552 GT:DR:DV 0/0:268491:27 +chr20 4687171 52 TCCGAGGGGGG N . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4687182;STD_quant_start=1.000000;STD_quant_stop=1.612452;Kurtosis_quant_start=-1.826820;Kurtosis_quant_stop=-2.058713;SVTYPE=DEL;SUPTYPE=AL;SVLEN=-11;STRANDS=+-;STRANDS2=3,18,3,18;RE=21;REF_strand=111064,157270;Strandbias_pval=0.0131367;AF=7.82607e-05 GT:DR:DV 0/0:268313:21 +chr20 4687187 53 TTGCGGCCGTT N . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4687201;STD_quant_start=5.399309;STD_quant_stop=4.883386;Kurtosis_quant_start=-1.875388;Kurtosis_quant_stop=-0.762039;SVTYPE=DEL;SUPTYPE=AL;SVLEN=-14;STRANDS=+-;STRANDS2=50,69,50,69;RE=119;REF_strand=110966,157275;Strandbias_pval=0.925905;AF=0.000443631 GT:DR:DV 0/0:268122:119 +chr20 4687272 54 GGGGAGGCCCCACCCTCTGTTCTCCAGGGGCGGGGAGAGAGGAGCTGCAGGTCTGCGGCCTGGCCCCAGGTGCGATGGCGGACCCCAGCTTGGCCAGTCACATTCCTCCCAGTCCCCCTGGAGGGAGAACGCTGGCCATGGGGGGCTCCAAGGAACAACCAGCCTCGGATGA N . PASS IMPRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4687430;STD_quant_start=19.508972;STD_quant_stop=25.830215;Kurtosis_quant_start=-0.929520;Kurtosis_quant_stop=-1.282851;SVTYPE=DEL;SUPTYPE=AL,NR;SVLEN=-158;STRANDS=+-;STRANDS2=6,4,6,4;RE=10;REF_strand=110054,157277;Strandbias_pval=0.335607;AF=3.74068e-05 GT:DR:DV 0/0:267321:10 +chr20 4687360 55 ACCCCAGCTTGGCCAGTCACATTCCTCCCAGTCCCCCTGGAGGGAGAACGC N . PASS IMPRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4687413;STD_quant_start=10.922454;STD_quant_stop=15.430489;Kurtosis_quant_start=-1.392600;Kurtosis_quant_stop=1.358093;SVTYPE=DEL;SUPTYPE=AL;SVLEN=-53;STRANDS=+-;STRANDS2=5,5,5,5;RE=10;REF_strand=109832,157278;Strandbias_pval=0.749822;AF=3.74378e-05 GT:DR:DV 0/0:267100:10 +chr20 4687388 56 N GGCGTATGCTGCTG . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4687398;STD_quant_start=7.942098;STD_quant_stop=8.076557;Kurtosis_quant_start=-1.966233;Kurtosis_quant_stop=-1.838604;SVTYPE=INS;SUPTYPE=AL;SVLEN=11;STRANDS=+-;STRANDS2=11,15,11,15;RE=26;REF_strand=109792,157278;Strandbias_pval=1;AF=9.73528e-05 GT:DR:DV 0/0:267044:26 +chr20 4687424 57 TCCAAGGAACAACCAGCCTCGGATG N . PASS IMPRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4687462;STD_quant_start=12.267844;STD_quant_stop=15.423509;Kurtosis_quant_start=-2.055059;Kurtosis_quant_stop=-1.936120;SVTYPE=DEL;SUPTYPE=AL;SVLEN=-38;STRANDS=+-;STRANDS2=92,116,92,116;RE=208;REF_strand=109557,157277;Strandbias_pval=0.359961;AF=0.000779511 GT:DR:DV 0/0:266626:208 +chr20 4687453 58 TTGGGTCACCGGTCTCCCCACCTGTGCGGCAGG N . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4687501;STD_quant_start=8.479387;STD_quant_stop=8.769265;Kurtosis_quant_start=-1.204235;Kurtosis_quant_stop=-1.240479;SVTYPE=DEL;SUPTYPE=AL,NR;SVLEN=-48;STRANDS=+-;STRANDS2=10,8,10,8;RE=18;REF_strand=109339,157274;Strandbias_pval=0.235607;AF=6.75136e-05 GT:DR:DV 0/0:266595:18 +chr20 4687584 59 TAGATTTTTTT N . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4687597;STD_quant_start=4.829893;STD_quant_stop=3.761322;Kurtosis_quant_start=-0.972723;Kurtosis_quant_stop=-1.612619;SVTYPE=DEL;SUPTYPE=AL,NR;SVLEN=-13;STRANDS=+-;STRANDS2=42,80,42,80;RE=122;REF_strand=108493,157272;Strandbias_pval=0.167099;AF=0.000459052 GT:DR:DV 0/0:265643:122 +chr20 4687590 60 N TTTTTTTTTTTTTTTTTTTT . STRANDBIAS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4687590;STD_quant_start=0.000000;STD_quant_stop=1.183216;Kurtosis_quant_start=0.361962;Kurtosis_quant_stop=-0.072859;SVTYPE=INS;SUPTYPE=AL;SVLEN=12;STRANDS=+-;STRANDS2=101,10,101,10;RE=111;REF_strand=108480,157272;Strandbias_pval=1.48889e-28;AF=0.000417683 GT:DR:DV 0/0:265641:111 +chr20 4687673 61 GCCTCCAGATT N . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4687688;STD_quant_start=2.934469;STD_quant_stop=2.345208;Kurtosis_quant_start=-0.528540;Kurtosis_quant_stop=0.078484;SVTYPE=DEL;SUPTYPE=AL,NR;SVLEN=-15;STRANDS=+-;STRANDS2=12,25,12,25;RE=37;REF_strand=107937,157266;Strandbias_pval=0.402981;AF=0.000139516 GT:DR:DV 0/0:265166:37 +chr20 4687703 62 N CGGAGAAGAATAATGGATATGACAC . PASS IMPRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4687736;STD_quant_start=14.236720;STD_quant_stop=10.923177;Kurtosis_quant_start=-2.063560;Kurtosis_quant_stop=-1.943954;SVTYPE=INS;SUPTYPE=AL;SVLEN=11;STRANDS=+-;STRANDS2=21,18,21,18;RE=39;REF_strand=107662,157262;Strandbias_pval=0.103791;AF=0.000147212 GT:DR:DV 0/0:264885:39 +chr20 4687773 63 N TTATTGAAAGTTAATGTTTC . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4687777;STD_quant_start=5.727128;STD_quant_stop=6.188699;Kurtosis_quant_start=1.059111;Kurtosis_quant_stop=3.582677;SVTYPE=INS;SUPTYPE=AL;SVLEN=12;STRANDS=+-;STRANDS2=6,5,6,5;RE=11;REF_strand=107279,157260;Strandbias_pval=0.370574;AF=4.15818e-05 GT:DR:DV 0/0:264528:11 +chr20 4687783 64 CCCATATGATTTGAAG N . PASS IMPRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4687828;STD_quant_start=12.909448;STD_quant_stop=11.523666;Kurtosis_quant_start=-1.823314;Kurtosis_quant_stop=-2.087287;SVTYPE=DEL;SUPTYPE=AL;SVLEN=-45;STRANDS=+-;STRANDS2=53,104,53,104;RE=157;REF_strand=107062,157259;Strandbias_pval=0.0880855;AF=0.000593975 GT:DR:DV 0/0:264164:157 +chr20 4687801 65 N TTTTTTTTTTTT . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4687803;STD_quant_start=6.833740;STD_quant_stop=6.268971;Kurtosis_quant_start=-1.631034;Kurtosis_quant_stop=-1.247564;SVTYPE=INS;SUPTYPE=AL;SVLEN=11;STRANDS=+-;STRANDS2=12,7,12,7;RE=19;REF_strand=107057,157260;Strandbias_pval=0.0596547;AF=7.18834e-05 GT:DR:DV 0/0:264298:19 +chr20 4687912 66 N AAAAAAAAAAAAAAAAAAAAAAAA . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4687923;STD_quant_start=8.508463;STD_quant_stop=6.350853;Kurtosis_quant_start=-1.829542;Kurtosis_quant_stop=-1.602699;SVTYPE=INS;SUPTYPE=AL;SVLEN=12;STRANDS=+-;STRANDS2=26,40,26,40;RE=66;REF_strand=106330,157250;Strandbias_pval=0.900944;AF=0.000250398 GT:DR:DV 0/0:263514:66 +chr20 4687949 67 N AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAACA . STRANDBIAS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4687952;STD_quant_start=0.000000;STD_quant_stop=1.732051;Kurtosis_quant_start=0.038940;Kurtosis_quant_stop=1.042296;SVTYPE=INS;SUPTYPE=AL;SVLEN=11;STRANDS=+-;STRANDS2=6,31,6,31;RE=37;REF_strand=106088,157224;Strandbias_pval=0.00226497;AF=0.000140518 GT:DR:DV 0/0:263275:37 +chr20 4687941 68 AGAAGAAAGGAAAA N . PASS IMPRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4688005;STD_quant_start=14.603082;STD_quant_stop=10.524970;Kurtosis_quant_start=-1.968426;Kurtosis_quant_stop=-1.785903;SVTYPE=DEL;SUPTYPE=AL;SVLEN=-64;STRANDS=+-;STRANDS2=63,98,63,98;RE=161;REF_strand=105750,157147;Strandbias_pval=0.809778;AF=0.000612407 GT:DR:DV 0/0:262736:161 +chr20 4688011 69 N AAAAAAAAAAAAAAA . STRANDBIAS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4688011;STD_quant_start=0.000000;STD_quant_stop=2.386557;Kurtosis_quant_start=0.550212;Kurtosis_quant_stop=-1.086567;SVTYPE=INS;SUPTYPE=AL;SVLEN=11;STRANDS=+-;STRANDS2=9,38,9,38;RE=47;REF_strand=105136,156884;Strandbias_pval=0.00273836;AF=0.000179376 GT:DR:DV 0/0:261973:47 diff --git a/SVs_sniffles/vcf/58778_bodySnif.vcf b/SVs_sniffles/vcf/58778_bodySnif.vcf new file mode 100644 index 0000000..f998c45 --- /dev/null +++ b/SVs_sniffles/vcf/58778_bodySnif.vcf @@ -0,0 +1,38 @@ +##fileformat=VCFv4.1 +##source=Sniffles +##fileDate=20210810:59:33 AMef_minus +##contig= +##ALT= +##ALT= +##ALT= +##ALT= +##ALT= +##ALT= +##FILTER= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##FORMAT= +##FORMAT= +##FORMAT= +#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT bamfilt/58778_f.bam +chr20 4699380 0 N GGTGGTGGCTGGGGGCAGCCCTCAT . STRANDBIAS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4699380;STD_quant_start=1.460593;STD_quant_stop=1.890922;Kurtosis_quant_start=-1.322054;Kurtosis_quant_stop=-1.330095;SVTYPE=INS;SUPTYPE=AL;SVLEN=24;STRANDS=+-;STRANDS2=1075,1056,1075,1056;RE=2131;REF_strand=6578,7406;Strandbias_pval=0.00360127;AF=0.152388 GT:DR:DV 0/0:11853:2131 +chr20 4699439 1 N GGGGCAGCCTCATGGGTAGGCT . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4699439;STD_quant_start=0.964421;STD_quant_stop=1.444307;Kurtosis_quant_start=0.557081;Kurtosis_quant_stop=0.559931;SVTYPE=INS;SUPTYPE=AL;SVLEN=23;STRANDS=+-;STRANDS2=346,398,346,398;RE=744;REF_strand=6578,7406;Strandbias_pval=0.791957;AF=0.0532037 GT:DR:DV 0/0:13240:744 diff --git a/SVs_sniffles/vcf/58778_promoterSnif.vcf b/SVs_sniffles/vcf/58778_promoterSnif.vcf new file mode 100644 index 0000000..fdc7558 --- /dev/null +++ b/SVs_sniffles/vcf/58778_promoterSnif.vcf @@ -0,0 +1,101 @@ +##fileformat=VCFv4.1 +##source=Sniffles +##fileDate=20210811:59:38 AMef_minus +##contig= +##ALT= +##ALT= +##ALT= +##ALT= +##ALT= +##ALT= +##FILTER= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##FORMAT= +##FORMAT= +##FORMAT= +#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT promoterbamfilt/58778_f.bam +chr20 4685109 0 CCTGGCTTCTC N . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4685122;STD_quant_start=4.953113;STD_quant_stop=6.150881;Kurtosis_quant_start=-0.521100;Kurtosis_quant_stop=-1.225451;SVTYPE=DEL;SUPTYPE=AL;SVLEN=-13;STRANDS=+-;STRANDS2=51,9,51,9;RE=60;REF_strand=149849,20970;Strandbias_pval=0.552381;AF=0.000351249 GT:DR:DV 0/0:170759:60 +chr20 4685131 1 N TGTTGAAAAACTGATATTATTATTCTACTTT . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4685143;STD_quant_start=6.051065;STD_quant_stop=7.168306;Kurtosis_quant_start=-1.288862;Kurtosis_quant_stop=-1.639307;SVTYPE=INS;SUPTYPE=AL;SVLEN=11;STRANDS=+-;STRANDS2=23,3,23,3;RE=26;REF_strand=149910,20999;Strandbias_pval=1;AF=0.000152128 GT:DR:DV 0/0:170883:26 +chr20 4685149 2 CTGCAACTTGA N . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4685161;STD_quant_start=6.543560;STD_quant_stop=6.888726;Kurtosis_quant_start=-2.071927;Kurtosis_quant_stop=-1.631896;SVTYPE=DEL;SUPTYPE=AL;SVLEN=-12;STRANDS=+-;STRANDS2=16,7,16,7;RE=23;REF_strand=149935,21020;Strandbias_pval=0.0173876;AF=0.000134538 GT:DR:DV 0/0:170932:23 +chr20 4685224 3 TTTTTTTTTTTT N . STRANDBIAS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4685235;STD_quant_start=0.000000;STD_quant_stop=0.347105;Kurtosis_quant_start=3.010894;Kurtosis_quant_stop=4.051334;SVTYPE=DEL;SUPTYPE=AL,NR;SVLEN=-11;STRANDS=+-;STRANDS2=456,42,456,42;RE=498;REF_strand=149986,21096;Strandbias_pval=0.00758312;AF=0.00291088 GT:DR:DV 0/0:170584:498 +chr20 4685224 4 N TTTTTTTTTTTTTTTTTT . STRANDBIAS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4685224;STD_quant_start=0.000000;STD_quant_stop=1.338344;Kurtosis_quant_start=46.754783;Kurtosis_quant_stop=1.310150;SVTYPE=INS;SUPTYPE=AL;SVLEN=11;STRANDS=+-;STRANDS2=7761,26,7761,26;RE=7787;REF_strand=149982,21088;Strandbias_pval=0;AF=0.0455194 GT:DR:DV 0/0:163283:7787 +chr20 4685224 5 TTTTTTTTTTTTT N . STRANDBIAS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4685238;STD_quant_start=0.000000;STD_quant_stop=0.750757;Kurtosis_quant_start=1.415551;Kurtosis_quant_stop=1.596411;SVTYPE=DEL;SUPTYPE=AL,NR;SVLEN=-14;STRANDS=+-;STRANDS2=253,78,253,78;RE=331;REF_strand=149987,21097;Strandbias_pval=1.98497e-08;AF=0.00193472 GT:DR:DV 0/0:170753:331 +chr20 4685337 6 N TCTCTCTGCCTGCGGTAA . PASS IMPRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4685353;STD_quant_start=11.366618;STD_quant_stop=6.172520;Kurtosis_quant_start=-1.997741;Kurtosis_quant_stop=-1.376556;SVTYPE=INS;SUPTYPE=AL;SVLEN=13;STRANDS=+-;STRANDS2=20,0,20,0;RE=20;REF_strand=150081,21201;Strandbias_pval=0.163051;AF=0.000116767 GT:DR:DV 0/0:171262:20 +chr20 4685412 7 TTTTTTTTATT N . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4685424;STD_quant_start=5.503246;STD_quant_stop=2.267787;Kurtosis_quant_start=-1.391070;Kurtosis_quant_stop=-1.371626;SVTYPE=DEL;SUPTYPE=AL;SVLEN=-12;STRANDS=+-;STRANDS2=48,8,48,8;RE=56;REF_strand=150088,21241;Strandbias_pval=0.683249;AF=0.000326857 GT:DR:DV 0/0:171273:56 +chr20 4685413 8 N TTTTTTTTTTTT . STRANDBIAS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4685413;STD_quant_start=0.000000;STD_quant_stop=4.854644;Kurtosis_quant_start=1.252421;Kurtosis_quant_stop=-1.012033;SVTYPE=INS;SUPTYPE=AL;SVLEN=11;STRANDS=+-;STRANDS2=211,11,211,11;RE=222;REF_strand=150088,21238;Strandbias_pval=0.000313869;AF=0.00129578 GT:DR:DV 0/0:171104:222 +chr20 4685413 9 TTTTTTTTATTTTTTGTAGAAATGGGGTCTCAC N . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4685445;STD_quant_start=4.832488;STD_quant_stop=9.133004;Kurtosis_quant_start=-1.952416;Kurtosis_quant_stop=-0.907211;SVTYPE=DEL;SUPTYPE=AL,NR;SVLEN=-32;STRANDS=+-;STRANDS2=30,4,30,4;RE=34;REF_strand=150088,21249;Strandbias_pval=1;AF=0.000198439 GT:DR:DV 0/0:171303:34 +chr20 4685538 10 TCAACATTCTTAAATCTCTTTCCTTAC N . PASS IMPRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4685579;STD_quant_start=11.566696;STD_quant_stop=12.047981;Kurtosis_quant_start=-1.943815;Kurtosis_quant_stop=-1.617600;SVTYPE=DEL;SUPTYPE=AL;SVLEN=-41;STRANDS=+-;STRANDS2=92,13,92,13;RE=105;REF_strand=150090,21311;Strandbias_pval=1;AF=0.000612599 GT:DR:DV 0/0:171296:105 +chr20 4685570 11 TTCCTAAACCTCT N . PASS IMPRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4685594;STD_quant_start=10.099505;STD_quant_stop=9.843780;Kurtosis_quant_start=-2.070963;Kurtosis_quant_stop=-1.568337;SVTYPE=DEL;SUPTYPE=AL;SVLEN=-24;STRANDS=+-;STRANDS2=19,0,19,0;RE=19;REF_strand=150090,21324;Strandbias_pval=0.157848;AF=0.000110843 GT:DR:DV 0/0:171395:19 +chr20 4685564 12 N AAAAAAAAAAAAAAAAAAA . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4685572;STD_quant_start=8.080842;STD_quant_stop=8.706320;Kurtosis_quant_start=-1.106886;Kurtosis_quant_stop=-1.722370;SVTYPE=INS;SUPTYPE=AL;SVLEN=11;STRANDS=+-;STRANDS2=12,3,12,3;RE=15;REF_strand=150090,21320;Strandbias_pval=0.42049;AF=8.75095e-05 GT:DR:DV 0/0:171395:15 +chr20 4685621 13 TGCCTGGTTTAC N . STRANDBIAS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4685647;STD_quant_start=8.065210;STD_quant_stop=5.629429;Kurtosis_quant_start=-1.862782;Kurtosis_quant_stop=-1.311458;SVTYPE=DEL;SUPTYPE=AL;SVLEN=-26;STRANDS=+-;STRANDS2=65,19,65,19;RE=84;REF_strand=150091,21347;Strandbias_pval=0.00791214;AF=0.000489973 GT:DR:DV 0/0:171354:84 +chr20 4685773 14 N AGAGATTTTCTGC . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4685780;STD_quant_start=7.675226;STD_quant_stop=4.719399;Kurtosis_quant_start=-1.740122;Kurtosis_quant_stop=-1.254667;SVTYPE=INS;SUPTYPE=AL;SVLEN=13;STRANDS=+-;STRANDS2=18,4,18,4;RE=22;REF_strand=150094,21446;Strandbias_pval=0.345851;AF=0.00012825 GT:DR:DV 0/0:171518:22 +chr20 4685777 15 CGCAAGAACACACCAC N . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4685793;STD_quant_start=2.325383;STD_quant_stop=3.511885;Kurtosis_quant_start=-1.151239;Kurtosis_quant_stop=-1.250294;SVTYPE=DEL;SUPTYPE=AL;SVLEN=-16;STRANDS=+-;STRANDS2=48,7,48,7;RE=55;REF_strand=150094,21451;Strandbias_pval=1;AF=0.000320616 GT:DR:DV 0/0:171490:55 +chr20 4685835 16 N TTTTTTTTTTTTTTTTTTTTTTTTTTT . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4685848;STD_quant_start=2.435843;STD_quant_stop=6.819091;Kurtosis_quant_start=-1.202728;Kurtosis_quant_stop=-1.691871;SVTYPE=INS;SUPTYPE=AL;SVLEN=11;STRANDS=+-;STRANDS2=58,2,58,2;RE=60;REF_strand=150094,21479;Strandbias_pval=0.0296532;AF=0.000349705 GT:DR:DV 0/0:171513:60 +chr20 4685865 17 TTAATATCACCACCTAAATCAT N . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4685882;STD_quant_start=5.981743;STD_quant_stop=7.167636;Kurtosis_quant_start=-1.961933;Kurtosis_quant_stop=-1.818774;SVTYPE=DEL;SUPTYPE=AL;SVLEN=-17;STRANDS=+-;STRANDS2=60,4,60,4;RE=64;REF_strand=150092,21498;Strandbias_pval=0.182508;AF=0.000372982 GT:DR:DV 0/0:171526:64 +chr20 4685898 18 N AAAAAAAAAAAAAAAAAAA . PASS IMPRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4685910;STD_quant_start=13.183323;STD_quant_stop=10.295630;Kurtosis_quant_start=-1.367188;Kurtosis_quant_stop=-1.330204;SVTYPE=INS;SUPTYPE=AL;SVLEN=11;STRANDS=+-;STRANDS2=9,3,9,3;RE=12;REF_strand=150090,21515;Strandbias_pval=0.183185;AF=6.9928e-05 GT:DR:DV 0/0:171593:12 +chr20 4685937 19 GTCAGTGTCCTT N . STRANDBIAS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4685951;STD_quant_start=4.789101;STD_quant_stop=5.713594;Kurtosis_quant_start=-1.726215;Kurtosis_quant_stop=-1.701394;SVTYPE=DEL;SUPTYPE=AL;SVLEN=-14;STRANDS=+-;STRANDS2=46,17,46,17;RE=63;REF_strand=150067,21538;Strandbias_pval=0.00177719;AF=0.000367122 GT:DR:DV 0/0:171542:63 +chr20 4686021 20 N TTTTTTTTTTTTTT . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4686022;STD_quant_start=3.694193;STD_quant_stop=5.724046;Kurtosis_quant_start=-1.682182;Kurtosis_quant_stop=-1.806783;SVTYPE=INS;SUPTYPE=AL;SVLEN=12;STRANDS=+-;STRANDS2=32,2,32,2;RE=34;REF_strand=149641,21599;Strandbias_pval=0.308371;AF=0.000198552 GT:DR:DV 0/0:171206:34 +chr20 4686075 21 CCTCATTCCTGAG N . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4686088;STD_quant_start=2.265969;STD_quant_stop=2.818210;Kurtosis_quant_start=-0.225904;Kurtosis_quant_stop=-0.482195;SVTYPE=DEL;SUPTYPE=AL;SVLEN=-13;STRANDS=+-;STRANDS2=95,9,95,9;RE=104;REF_strand=149298,21633;Strandbias_pval=0.29957;AF=0.000608433 GT:DR:DV 0/0:170827:104 +chr20 4686092 22 N TTTTTTTTTTTTTTT . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4686099;STD_quant_start=3.184785;STD_quant_stop=4.992852;Kurtosis_quant_start=-1.359980;Kurtosis_quant_stop=-1.762926;SVTYPE=INS;SUPTYPE=AL;SVLEN=11;STRANDS=+-;STRANDS2=26,3,26,3;RE=29;REF_strand=149229,21640;Strandbias_pval=1;AF=0.000169721 GT:DR:DV 0/0:170840:29 +chr20 4686134 23 N TGGCGAGAGATTTTA . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4686151;STD_quant_start=5.984829;STD_quant_stop=8.458455;Kurtosis_quant_start=-2.018021;Kurtosis_quant_stop=-2.004952;SVTYPE=INS;SUPTYPE=AL;SVLEN=12;STRANDS=+-;STRANDS2=23,0,23,0;RE=23;REF_strand=148933,21666;Strandbias_pval=0.10654;AF=0.000134819 GT:DR:DV 0/0:170576:23 +chr20 4686182 24 N CATGTCATGCCCTGTCTGCCCTGT . PASS IMPRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4686202;STD_quant_start=11.376668;STD_quant_stop=13.087617;Kurtosis_quant_start=-1.627721;Kurtosis_quant_stop=-2.131127;SVTYPE=INS;SUPTYPE=AL;SVLEN=12;STRANDS=+-;STRANDS2=28,1,28,1;RE=29;REF_strand=148622,21712;Strandbias_pval=0.167995;AF=0.000170254 GT:DR:DV 0/0:170305:29 +chr20 4686230 25 TCAAGCGAATC N . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4686241;STD_quant_start=5.547772;STD_quant_stop=3.701851;Kurtosis_quant_start=-1.559920;Kurtosis_quant_stop=-1.772230;SVTYPE=DEL;SUPTYPE=AL;SVLEN=-11;STRANDS=+-;STRANDS2=41,13,41,13;RE=54;REF_strand=148363,21740;Strandbias_pval=0.0221873;AF=0.000317455 GT:DR:DV 0/0:170049:54 +chr20 4686249 26 N TTTTTTTTTTTT . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4686250;STD_quant_start=0.000000;STD_quant_stop=3.630677;Kurtosis_quant_start=-0.307806;Kurtosis_quant_stop=-1.023288;SVTYPE=INS;SUPTYPE=AL;SVLEN=11;STRANDS=+-;STRANDS2=44,1,44,1;RE=45;REF_strand=148239,21742;Strandbias_pval=0.0253936;AF=0.000264735 GT:DR:DV 0/0:169936:45 +chr20 4686362 27 N TCTTCACCAACCCGCCAC . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4686368;STD_quant_start=5.248376;STD_quant_stop=2.828427;Kurtosis_quant_start=-1.631730;Kurtosis_quant_stop=-1.561400;SVTYPE=INS;SUPTYPE=AL;SVLEN=13;STRANDS=+-;STRANDS2=20,2,20,2;RE=22;REF_strand=147443,21835;Strandbias_pval=1;AF=0.000129964 GT:DR:DV 0/0:169256:22 +chr20 4686405 28 CTTCCCCGCCCCGCGTCCCTCCCCCTCGGCCCCGCGCGTCGCCTGTCCTCCGAGCCAGTCGCTGACAGCCGCGGCGCCGCGA N . PASS IMPRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4686480;STD_quant_start=28.275431;STD_quant_stop=27.705595;Kurtosis_quant_start=-1.130570;Kurtosis_quant_stop=0.083732;SVTYPE=DEL;SUPTYPE=AL;SVLEN=-75;STRANDS=+-;STRANDS2=8,2,8,2;RE=10;REF_strand=146905,21894;Strandbias_pval=0.379252;AF=5.92421e-05 GT:DR:DV 0/0:168789:10 +chr20 4686365 29 CCCCGCGCCGACCTCCGCCCGCGAGCGCCGCCGCTTCCCTTCCCCGCCCCGCGTCCCTCCCCCTCGGC N . PASS IMPRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4686437;STD_quant_start=15.989412;STD_quant_stop=16.036249;Kurtosis_quant_start=-1.943824;Kurtosis_quant_stop=-1.950385;SVTYPE=DEL;SUPTYPE=AL;SVLEN=-72;STRANDS=+-;STRANDS2=202,46,202,46;RE=248;REF_strand=147194,21863;Strandbias_pval=0.0133656;AF=0.00146696 GT:DR:DV 0/0:168809:248 +chr20 4686463 30 N CTCCCTGCCACAGC . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4686470;STD_quant_start=6.681531;STD_quant_stop=4.855042;Kurtosis_quant_start=-1.835304;Kurtosis_quant_stop=-1.690394;SVTYPE=INS;SUPTYPE=AL;SVLEN=11;STRANDS=+-;STRANDS2=23,6,23,6;RE=29;REF_strand=146764,21912;Strandbias_pval=0.260682;AF=0.000171927 GT:DR:DV 0/0:168647:29 +chr20 4686486 31 CTTCTCCTCTCCTCA N . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4686501;STD_quant_start=3.066317;STD_quant_stop=4.068381;Kurtosis_quant_start=-0.988554;Kurtosis_quant_stop=-0.876508;SVTYPE=DEL;SUPTYPE=AL;SVLEN=-15;STRANDS=+-;STRANDS2=151,24,151,24;RE=175;REF_strand=146601,21923;Strandbias_pval=0.736532;AF=0.00103843 GT:DR:DV 0/0:168349:175 +chr20 4686550 32 N GGGGGGGGGGGG . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4686556;STD_quant_start=5.545268;STD_quant_stop=4.699291;Kurtosis_quant_start=-0.536539;Kurtosis_quant_stop=-1.070211;SVTYPE=INS;SUPTYPE=AL;SVLEN=11;STRANDS=+-;STRANDS2=21,3,21,3;RE=24;REF_strand=146179,21962;Strandbias_pval=1;AF=0.000142737 GT:DR:DV 0/0:168117:24 +chr20 4686589 33 CCCAGGCGCAAGGGTGCCCGGCCGGGCGGGGTCGGGACCCCAGTGAGGAG N . PASS IMPRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4686643;STD_quant_start=12.696456;STD_quant_stop=8.354639;Kurtosis_quant_start=-1.448567;Kurtosis_quant_stop=0.655015;SVTYPE=DEL;SUPTYPE=AL;SVLEN=-54;STRANDS=+-;STRANDS2=9,3,9,3;RE=12;REF_strand=145917,22025;Strandbias_pval=0.2014;AF=7.14532e-05 GT:DR:DV 0/0:167930:12 +chr20 4686607 34 N CGGTAGGCGATGTAG . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4686612;STD_quant_start=5.234501;STD_quant_stop=6.633250;Kurtosis_quant_start=-0.975553;Kurtosis_quant_stop=-0.912602;SVTYPE=INS;SUPTYPE=AL;SVLEN=11;STRANDS=+-;STRANDS2=17,0,17,0;RE=17;REF_strand=145940,22010;Strandbias_pval=0.153361;AF=0.000101221 GT:DR:DV 0/0:167933:17 +chr20 4686617 35 GGGTCGGGACCCCAGTGAGGAGGGGCC N . STRANDBIAS IMPRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4686648;STD_quant_start=14.319783;STD_quant_stop=8.625153;Kurtosis_quant_start=-1.899641;Kurtosis_quant_stop=-1.586561;SVTYPE=DEL;SUPTYPE=AL;SVLEN=-31;STRANDS=+-;STRANDS2=132,47,132,47;RE=179;REF_strand=145845,22033;Strandbias_pval=2.29959e-06;AF=0.00106625 GT:DR:DV 0/0:167699:179 +chr20 4686661 36 GACGCGTCTCGGGCCTGCCCGGCTGCGCTGGTCTCCGCTCGGGTGAGGCGGC N . PASS IMPRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4686707;STD_quant_start=3.924283;STD_quant_stop=21.042814;Kurtosis_quant_start=0.165513;Kurtosis_quant_stop=-2.298847;SVTYPE=DEL;SUPTYPE=AL;SVLEN=-46;STRANDS=+-;STRANDS2=16,2,16,2;RE=18;REF_strand=145590,22082;Strandbias_pval=1;AF=0.000107352 GT:DR:DV 0/0:167654:18 +chr20 4686672 37 N GTCACGCCTGCCGCCT . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4686675;STD_quant_start=3.015113;STD_quant_stop=4.622081;Kurtosis_quant_start=-1.675265;Kurtosis_quant_stop=-1.786869;SVTYPE=INS;SUPTYPE=AL;SVLEN=12;STRANDS=+-;STRANDS2=20,3,20,3;RE=23;REF_strand=145629,22076;Strandbias_pval=1;AF=0.000137146 GT:DR:DV 0/0:167682:23 +chr20 4686729 38 TTTTCAGGTTAGGAA N . PASS IMPRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4686760;STD_quant_start=2.915476;STD_quant_stop=10.202941;Kurtosis_quant_start=-1.289877;Kurtosis_quant_stop=-1.176694;SVTYPE=DEL;SUPTYPE=AL;SVLEN=-31;STRANDS=+-;STRANDS2=18,2,18,2;RE=20;REF_strand=145187,22126;Strandbias_pval=1;AF=0.000119536 GT:DR:DV 0/0:167293:20 +chr20 4686729 39 N TTTTTTTTTTTTTTTTTTTTT . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4686739;STD_quant_start=6.789029;STD_quant_stop=4.981785;Kurtosis_quant_start=-1.798168;Kurtosis_quant_stop=-1.659204;SVTYPE=INS;SUPTYPE=AL;SVLEN=11;STRANDS=+-;STRANDS2=20,2,20,2;RE=22;REF_strand=145248,22113;Strandbias_pval=0.759458;AF=0.000131452 GT:DR:DV 0/0:167339:22 +chr20 4686795 40 N TGCCCTTGCCTGCC . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4686798;STD_quant_start=3.783186;STD_quant_stop=5.442885;Kurtosis_quant_start=-1.610852;Kurtosis_quant_stop=-1.698554;SVTYPE=INS;SUPTYPE=AL;SVLEN=11;STRANDS=+-;STRANDS2=29,4,29,4;RE=33;REF_strand=144940,22174;Strandbias_pval=1;AF=0.00019747 GT:DR:DV 0/0:167081:33 +chr20 4686866 41 N CTCTATATTTTGTGTG . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4686874;STD_quant_start=7.867655;STD_quant_stop=7.328028;Kurtosis_quant_start=-1.592415;Kurtosis_quant_stop=-0.757039;SVTYPE=INS;SUPTYPE=AL;SVLEN=11;STRANDS=+-;STRANDS2=13,1,13,1;RE=14;REF_strand=144576,22224;Strandbias_pval=1;AF=8.39329e-05 GT:DR:DV 0/0:166786:14 +chr20 4686921 42 GGGCGGGGAGGGGCGCCTGGGGGCCGCGGGGCTCGCGCTCCCCGCCCGTTGGCCGC N . PASS IMPRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4686991;STD_quant_start=4.571652;STD_quant_stop=10.049876;Kurtosis_quant_start=0.494724;Kurtosis_quant_stop=-1.698374;SVTYPE=DEL;SUPTYPE=AL,NR;SVLEN=-70;STRANDS=+-;STRANDS2=19,2,19,2;RE=21;REF_strand=144015,22291;Strandbias_pval=1;AF=0.000126273 GT:DR:DV 0/0:166285:21 +chr20 4686928 43 GGGGCGCCTGGGGGC N . STRANDBIAS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4686944;STD_quant_start=2.477485;STD_quant_stop=2.834516;Kurtosis_quant_start=1.376895;Kurtosis_quant_stop=-0.450443;SVTYPE=DEL;SUPTYPE=AL,NR;SVLEN=-16;STRANDS=+-;STRANDS2=30,29,30,29;RE=59;REF_strand=144123,22276;Strandbias_pval=4.47183e-11;AF=0.000354569 GT:DR:DV 0/0:166340:59 +chr20 4686920 44 N CTAGCATTTACA . PASS IMPRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4686930;STD_quant_start=7.715785;STD_quant_stop=10.795061;Kurtosis_quant_start=-1.769925;Kurtosis_quant_stop=-1.969736;SVTYPE=INS;SUPTYPE=AL;SVLEN=11;STRANDS=+-;STRANDS2=28,2,28,2;RE=30;REF_strand=144173,22269;Strandbias_pval=0.420522;AF=0.000180243 GT:DR:DV 0/0:166412:30 +chr20 4686971 45 N CCTTAGCTAGC . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4686971;STD_quant_start=2.121320;STD_quant_stop=1.963961;Kurtosis_quant_start=-0.925674;Kurtosis_quant_stop=0.830811;SVTYPE=INS;SUPTYPE=AL;SVLEN=11;STRANDS=+-;STRANDS2=24,4,24,4;RE=28;REF_strand=143934,22302;Strandbias_pval=0.784137;AF=0.000168435 GT:DR:DV 0/0:166208:28 +chr20 4687051 46 N GGGGGGGGGGGGGGGGGGG . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4687051;STD_quant_start=4.483302;STD_quant_stop=5.176872;Kurtosis_quant_start=-1.274283;Kurtosis_quant_stop=-1.266325;SVTYPE=INS;SUPTYPE=AL;SVLEN=14;STRANDS=+-;STRANDS2=17,0,17,0;RE=17;REF_strand=143580,22372;Strandbias_pval=0.153392;AF=0.000102439 GT:DR:DV 0/0:165935:17 +chr20 4687066 47 GGGGCGCCCGCC N . STRANDBIAS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4687078;STD_quant_start=4.907477;STD_quant_stop=5.237684;Kurtosis_quant_start=-1.621558;Kurtosis_quant_stop=-1.786634;SVTYPE=DEL;SUPTYPE=AL;SVLEN=-12;STRANDS=+-;STRANDS2=76,44,76,44;RE=120;REF_strand=143481,22381;Strandbias_pval=1.60997e-10;AF=0.000723493 GT:DR:DV 0/0:165742:120 +chr20 4687128 48 GGCCCAGCCCTTCATCCTCGCCGCCTGAGCTTCTCCGAGGGGGGCTGCAGCCTTGCGGCCGTTGCCACCGCCTGGA N . PASS IMPRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4687217;STD_quant_start=11.379807;STD_quant_stop=9.974969;Kurtosis_quant_start=-0.735091;Kurtosis_quant_stop=-0.830015;SVTYPE=DEL;SUPTYPE=AL;SVLEN=-89;STRANDS=+-;STRANDS2=14,2,14,2;RE=16;REF_strand=143003,22428;Strandbias_pval=1;AF=9.67171e-05 GT:DR:DV 0/0:165415:16 +chr20 4687146 49 N CACGCGCCCCCTGC . PASS IMPRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4687154;STD_quant_start=10.034939;STD_quant_stop=7.784600;Kurtosis_quant_start=-1.974370;Kurtosis_quant_stop=-1.887108;SVTYPE=INS;SUPTYPE=AL;SVLEN=13;STRANDS=+-;STRANDS2=16,3,16,3;RE=19;REF_strand=143123,22436;Strandbias_pval=0.735847;AF=0.000114763 GT:DR:DV 0/0:165540:19 +chr20 4687212 50 GCCACCGCCTGGAGAAGCGGCCCACGCGGACTGACGGGCGGGGGCGGGGCCTCGGGCCTCGGCGGGGGCGGGGTCCGGGGAGGCCCCAC N . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4687290;STD_quant_start=7.949843;STD_quant_stop=9.077445;Kurtosis_quant_start=0.584400;Kurtosis_quant_stop=-0.763115;SVTYPE=DEL;SUPTYPE=AL;SVLEN=-78;STRANDS=+-;STRANDS2=10,3,10,3;RE=13;REF_strand=142562,22433;Strandbias_pval=0.405042;AF=7.87903e-05 GT:DR:DV 0/0:164982:13 +chr20 4687241 51 N ACCAACCCCAGCTCCCTGTTTC . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4687248;STD_quant_start=7.395945;STD_quant_stop=7.169379;Kurtosis_quant_start=-2.028909;Kurtosis_quant_stop=-1.772655;SVTYPE=INS;SUPTYPE=AL;SVLEN=11;STRANDS=+-;STRANDS2=17,2,17,2;RE=19;REF_strand=142643,22432;Strandbias_pval=1;AF=0.000115099 GT:DR:DV 0/0:165056:19 +chr20 4687275 52 CCGGGGAGGCC N . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4687286;STD_quant_start=4.166410;STD_quant_stop=4.444097;Kurtosis_quant_start=-1.464870;Kurtosis_quant_stop=-1.510618;SVTYPE=DEL;SUPTYPE=AL,NR;SVLEN=-11;STRANDS=+-;STRANDS2=257,55,257,55;RE=312;REF_strand=142348,22432;Strandbias_pval=0.0468446;AF=0.00189343 GT:DR:DV 0/0:164468:312 +chr20 4687441 53 TCGGATGACGACCCTTGGGTCACCGGT N . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4687468;STD_quant_start=5.928141;STD_quant_stop=9.639947;Kurtosis_quant_start=-0.579609;Kurtosis_quant_stop=-1.593327;SVTYPE=DEL;SUPTYPE=AL,NR;SVLEN=-27;STRANDS=+-;STRANDS2=22,7,22,7;RE=29;REF_strand=141677,22432;Strandbias_pval=0.105445;AF=0.000176712 GT:DR:DV 0/0:164080:29 +chr20 4687473 54 N CACCACACACACA . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4687474;STD_quant_start=2.958040;STD_quant_stop=3.500000;Kurtosis_quant_start=-1.625068;Kurtosis_quant_stop=-1.751233;SVTYPE=INS;SUPTYPE=AL;SVLEN=11;STRANDS=+-;STRANDS2=20,5,20,5;RE=25;REF_strand=141596,22432;Strandbias_pval=0.376245;AF=0.000152413 GT:DR:DV 0/0:164003:25 +chr20 4687447 55 CACCGGTCTCCCCACCTGTGCGGCAGG N . PASS IMPRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4687501;STD_quant_start=14.971401;STD_quant_stop=6.484414;Kurtosis_quant_start=-1.767304;Kurtosis_quant_stop=-1.684365;SVTYPE=DEL;SUPTYPE=AL;SVLEN=-54;STRANDS=+-;STRANDS2=79,5,79,5;RE=84;REF_strand=141584,22432;Strandbias_pval=0.0380228;AF=0.000512145 GT:DR:DV 0/0:163932:84 +chr20 4687540 56 N TTTTTTTTTTTTTTTTTTTT . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4687540;STD_quant_start=4.301163;STD_quant_stop=7.286975;Kurtosis_quant_start=0.279509;Kurtosis_quant_stop=1.192206;SVTYPE=INS;SUPTYPE=AL;SVLEN=17;STRANDS=+-;STRANDS2=10,2,10,2;RE=12;REF_strand=141266,22432;Strandbias_pval=0.674955;AF=7.33057e-05 GT:DR:DV 0/0:163686:12 +chr20 4687590 57 N TTTTTTTTTTTTTTTT . STRANDBIAS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4687590;STD_quant_start=0.000000;STD_quant_stop=1.029332;Kurtosis_quant_start=0.425862;Kurtosis_quant_stop=-0.506709;SVTYPE=INS;SUPTYPE=AL;SVLEN=12;STRANDS=+-;STRANDS2=168,1,168,1;RE=169;REF_strand=141038,22432;Strandbias_pval=7.39962e-10;AF=0.00103383 GT:DR:DV 0/0:163301:169 +chr20 4687635 58 TCGCAGAGCCACAGCTCTCCG N . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4687660;STD_quant_start=9.567100;STD_quant_stop=5.487955;Kurtosis_quant_start=-1.930936;Kurtosis_quant_stop=-1.447783;SVTYPE=DEL;SUPTYPE=AL;SVLEN=-25;STRANDS=+-;STRANDS2=54,14,54,14;RE=68;REF_strand=140835,22432;Strandbias_pval=0.111185;AF=0.000416496 GT:DR:DV 0/0:163199:68 +chr20 4687660 59 N TTTTTTTTTTTTTT . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4687665;STD_quant_start=0.267261;STD_quant_stop=5.216731;Kurtosis_quant_start=-1.006664;Kurtosis_quant_stop=-1.941713;SVTYPE=INS;SUPTYPE=AL;SVLEN=11;STRANDS=+-;STRANDS2=27,2,27,2;RE=29;REF_strand=140759,22432;Strandbias_pval=0.419027;AF=0.000177706 GT:DR:DV 0/0:163162:29 +chr20 4687726 60 TCTTCATGGCCG N . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4687749;STD_quant_start=6.084870;STD_quant_stop=5.793453;Kurtosis_quant_start=-1.542432;Kurtosis_quant_stop=-1.143039;SVTYPE=DEL;SUPTYPE=AL;SVLEN=-23;STRANDS=+-;STRANDS2=73,6,73,6;RE=79;REF_strand=140469,22432;Strandbias_pval=0.139658;AF=0.000484957 GT:DR:DV 0/0:162822:79 +chr20 4687743 61 N TTTTTTTTTTTTTG . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4687747;STD_quant_start=5.449065;STD_quant_stop=5.811130;Kurtosis_quant_start=-1.854230;Kurtosis_quant_stop=-1.803138;SVTYPE=INS;SUPTYPE=AL;SVLEN=11;STRANDS=+-;STRANDS2=24,3,24,3;RE=27;REF_strand=140446,22432;Strandbias_pval=1;AF=0.000165768 GT:DR:DV 0/0:162851:27 +chr20 4687830 62 N . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4687857;STD_quant_start=5.760658;STD_quant_stop=6.938887;Kurtosis_quant_start=-1.487234;Kurtosis_quant_stop=-0.615471;SVTYPE=DEL;SUPTYPE=AL;SVLEN=-27;STRANDS=+-;STRANDS2=43,12,43,12;RE=55;REF_strand=139947,22430;Strandbias_pval=0.113559;AF=0.000338718 GT:DR:DV 0/0:162322:55 +chr20 4687877 63 N . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4687892;STD_quant_start=3.331666;STD_quant_stop=2.792848;Kurtosis_quant_start=0.702613;Kurtosis_quant_stop=0.113145;SVTYPE=DEL;SUPTYPE=AL;SVLEN=-15;STRANDS=+-;STRANDS2=13,7,13,7;RE=20;REF_strand=139767,22428;Strandbias_pval=0.0143855;AF=0.000123308 GT:DR:DV 0/0:162175:20 +chr20 4687985 64 N . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4688005;STD_quant_start=6.928203;STD_quant_stop=5.576737;Kurtosis_quant_start=-2.087095;Kurtosis_quant_stop=-1.801389;SVTYPE=DEL;SUPTYPE=AL;SVLEN=-20;STRANDS=+-;STRANDS2=36,5,36,5;RE=41;REF_strand=138819,22395;Strandbias_pval=1;AF=0.00025432 GT:DR:DV 0/0:161173:41 diff --git a/SVs_sniffles/vcf/59060_bodySnif.vcf b/SVs_sniffles/vcf/59060_bodySnif.vcf new file mode 100644 index 0000000..2b7f5ae --- /dev/null +++ b/SVs_sniffles/vcf/59060_bodySnif.vcf @@ -0,0 +1,40 @@ +##fileformat=VCFv4.1 +##source=Sniffles +##fileDate=20210810:59:52 AMef_minus +##contig= +##ALT= +##ALT= +##ALT= +##ALT= +##ALT= +##ALT= +##FILTER= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##FORMAT= +##FORMAT= +##FORMAT= +#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT bamfilt/59060_f.bam +chr20 4699380 0 N GGTGGTGGCTGGGGGCAGCCTCATGGTGGTGGCTGGGGGCAGCCTCATGGTGGCGGCTGGGGGCAGCCTCATGGTGGTGGCTGGGGGCAGCCCCATGGTGGTGGCTGGGGACCTCATGGTGGTGGCTGGGGGCAGCCCCCAT . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4699380;STD_quant_start=3.122605;STD_quant_stop=3.981889;Kurtosis_quant_start=-0.862096;Kurtosis_quant_stop=-0.548632;SVTYPE=INS;SUPTYPE=AL;SVLEN=142;STRANDS=+-;STRANDS2=612,896,612,896;RE=1508;REF_strand=5308,7618;Strandbias_pval=0.739939;AF=0.116664 GT:DR:DV 0/0:11418:1508 +chr20 4699380 1 N GGTGGGTAGCTGGGGGCAGCCTCAT . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4699380;STD_quant_start=4.477543;STD_quant_stop=5.162416;Kurtosis_quant_start=-1.170367;Kurtosis_quant_stop=-1.383447;SVTYPE=INS;SUPTYPE=AL;SVLEN=23;STRANDS=+-;STRANDS2=138,235,138,235;RE=373;REF_strand=5308,7618;Strandbias_pval=0.121498;AF=0.0288566 GT:DR:DV 0/0:12553:373 +chr20 4699439 2 N GGGCAGCCTCATGGTGGTGGCTGGGGGGCAGCCCCATGGTAGTGGCTGGGGACAGCCTCATGGTGGCTGGGGGCAGCCCCATGGTGGTGGCTGGGGCAGCCTCATGGTGGTGGCTGGGGGCAGCCTCATGGTGGTGGCT . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4699439;STD_quant_start=1.811715;STD_quant_stop=8.335850;Kurtosis_quant_start=-1.100281;Kurtosis_quant_stop=-0.936864;SVTYPE=INS;SUPTYPE=AL;SVLEN=142;STRANDS=+-;STRANDS2=219,370,219,370;RE=589;REF_strand=5308,7618;Strandbias_pval=0.0653231;AF=0.0455671 GT:DR:DV 0/0:12337:589 +chr20 4699463 3 N AAAAGCCCCATGGTAAGAGCTGGGGACAGCCTCATGGTGGCTGGGGGTCTCACAGGTGGCTGGGGGCAGCCTCATGGTGGTGGCTGGGGGCAGCCTCATGGTGGTGGCTGGGGCACCATGGCAGGTGC . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4699471;STD_quant_start=8.676392;STD_quant_stop=5.765260;Kurtosis_quant_start=-1.816939;Kurtosis_quant_stop=-1.415194;SVTYPE=INS;SUPTYPE=AL;SVLEN=118;STRANDS=+-;STRANDS2=311,412,311,412;RE=723;REF_strand=5308,7618;Strandbias_pval=0.312739;AF=0.0559338 GT:DR:DV 0/0:12203:723 diff --git a/SVs_sniffles/vcf/59060_promoterSnif.vcf b/SVs_sniffles/vcf/59060_promoterSnif.vcf new file mode 100644 index 0000000..1f72717 --- /dev/null +++ b/SVs_sniffles/vcf/59060_promoterSnif.vcf @@ -0,0 +1,37 @@ +##fileformat=VCFv4.1 +##source=Sniffles +##fileDate=20210812:02:21 PMef_minus +##contig= +##ALT= +##ALT= +##ALT= +##ALT= +##ALT= +##ALT= +##FILTER= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##FORMAT= +##FORMAT= +##FORMAT= +#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT promoterbamfilt/59060_f.bam +chr20 4685224 0 TTTTTTTTTTTTTTTT N . PASS PRECISE;SVMETHOD=Snifflesv1.0.12;CHR2=chr20;END=4685236;STD_quant_start=0.000000;STD_quant_stop=0.852803;Kurtosis_quant_start=1.791320;Kurtosis_quant_stop=1.801035;SVTYPE=DEL;SUPTYPE=AL;SVLEN=-12;STRANDS=+-;STRANDS2=13,10,13,10;RE=23;REF_strand=661,584;Strandbias_pval=0.834508;AF=0.0184739 GT:DR:DV 0/0:1222:23 diff --git a/controlPCR/conPCR_needleSam.R b/controlPCR/conPCR_needleSam.R new file mode 100644 index 0000000..bea2ecc --- /dev/null +++ b/controlPCR/conPCR_needleSam.R @@ -0,0 +1,1265 @@ +# Note, below is all taken directly from needleSam.R +# here, applied to the control PCR on sample #56635 +# will do as little modifications as possible, so will look convoluted as original script is applied on all the samples + +# needle in a SAM + +# finding a possible somatic mutation in the reads +# like a needle in a haystack! +# needle = somatic mutation / haystack = SAM files + +oprlength <- 123 +# threshold used in readSam() to exclude reads that start or terminate in the OPR by CIGAR lengths + + + +# some common things we may need to change often -------------------------- +hapcol <- 21 # nth field in the SAM file contains the HP tags (looks like HP:i:1; it was 20th then 21th in a newer version of minimap2) +hapcols <- c('#f1876b', '#4D4D4D', '#B3BDC4') # colours for the haplotypes, it goes 1, 2, 0 + + + +# packages and functions -------------------------------------------------- + + +library(here) +library(stringr) +library(data.table) +library(openxlsx) +library(msa) +library(ggplot2) +library(tictoc) +library(dplyr) +library(tidyr) +library(ggpubr) +library(ggbeeswarm) + +# substrEnding = last n characters of a string +# x = string (or vector of strings); n = last n characters +substrEnding <- function(x, n){ + substr(x, nchar(x)-n+1, nchar(x)) +} + +# beforeFirstCharacter = given a string, takes everything before first instance of a character +# eg. beforeFirstCharacter('59060_file.bam', '_') >> '59060' +beforeFirstCharacter <- function(stri, cha) { + as.character(sapply(stri, function(st){ + substr(st, + 1, + which(strsplit(st, '')[[1]] == cha) [length(which(strsplit(st, '')[[1]] == cha))]-1) + })) +} + +### + +# getReadlengthCigar() is a small helper function for readSam() below + # the goal is to exlude reads which start or terminate in the OPR + # these get categorised as reference because their CIGAR are for example 56M +# However, these reads do not span the whole OPR, so they should be excluded + # but excluding by readlength does not work, for example a 103-bp read could be a OPRD1 or a reference read that terminated early in the OPR +# one solution is to compute the alignment length as told by the CIGAR (only Match/Insertion/Deletion) + # this essentially corresponds to the window of hg38 that is covered by the read (as it will include deletions) + +# get read length as told by CIGAR +getReadlengthCigar <- function(read) { # works for one row of a sam file + cigar <- read[6] + tmp <- str_extract_all(cigar, '[0-9]+[MDI]')[[1]] # all the Match/Deletion/Insertion components of the CIGAR + rlci <- sum(as.numeric(unlist(strsplit(tmp, '[A-Z]')))) # rlci = readlength cigar + return(rlci) +} + +### + +# readSam = reads SAM properly into R +readSam <- function(sampath) { + + # check the path actually looks like it leads to a SAM file + if(substrEnding(sampath, 4) != '.sam') stop('\t \t \t \t >>> Error: that does not look like the path to a SAM file... \n') + + # if ok -- import the SAM file + # numcols <- max(count.fields(sampath, sep='\t'), na.rm=TRUE) + # above is to count maximum number of columns to be used below as sprintf('col%i', numcols) + # works well, but when importing more than one SAM, can have variable number of columns + # alternative: set to a large number. It will create NA columns at the end, but at least we know all the SAMs look the same + # (can delete the NA columns after rbind all the SAMs, if that is what we want to do) + sam <- read.table(file=sampath, fill=TRUE, comment.char='@', sep='\t', na.strings=c('', 'NA'), + col.names=sprintf('col%i', 1:30)) + + # check what should be the haplotype tag column, can be messy for different reasons + hpcol <- 21 + + taghp <- substr(sam[,hpcol], 1, 2) # will take mostly NA or HP and we do not want anything else, hence below + cat('\t \t \t \t \t >>> Found', length(which(taghp=='HP')), 'haplotags in the expected column \n') + + if (length(which(taghp!='HP')) > 0) { + cat('\t \t \t \t \t >>> Removed', length(which(taghp!='HP')), 'unexpected tags from the HP column \n') + sam[which(taghp!='HP'), hpcol] <- NA # the rows that are not NA or HP, replace them with NA + # ! for these rows, it is possible that the HP tag was pushed to the next column + # no need to look only at these rows, just look in the next column for any HP + taghpnxt <- substr(sam[,hpcol+1], 1, 2) + + if(length(which(taghpnxt=='HP')) > 0) { # if found any HP tag to salvage from the next column + cat('\t \t \t \t \t \t >>> for', length(which(taghpnxt=='HP')), 'of these reads, salvaged the HP tag found in the next column \n') + sam[which(taghpnxt=='HP'), hpcol+1] <- sam[which(taghpnxt=='HP'), hpcol+1] # copy it to the HP column + + # ! Note this is far from an ideal solution, will copy the HP tag and it also means the columns are shifted for these rows + # but at the moment I am not using any other tag than HP + } + } + + # check there is no HP tag in other columns before or after HP column + for (co in ((hpcol-4):(hpcol+4))[-5]) { # check all 4 columns before HP column, all 4 columns after HP column, except HP column itself + tagco <- substr(sam[,co], 1, 2) + if(length(which(tagco=='HP')) > 0) { + cat('\t \t \t \t \t >>> found ', length(which(tagco=='HP')), ' HP tags in column', co ,'\n') + } + } + + # check there is no duplicate read ID + # as I removed secondary alignments in filterBam.command it should be good + if (sum(duplicated(sam[1])) != 0) { + stop('\t \t \t \t \t >>> Error: found', sum(duplicated(sam[1])), 'duplicated read IDs \n') + } else { + cat('\t \t \t \t \t >>> All read IDs are unique \n') + } + + # exclude reads that start or terminate in the OPR (see explanations for getReadlengthCigar() above) + reads2del <- which(apply(sam, 1, getReadlengthCigar) < oprlength) + + if (length(reads2del) == 0) { + cat('\t \t \t \t \t >>> 0 read that start or terminate in the OPR \n') + } else { + cat('\t \t \t \t \t >>> Deleting', length(reads2del),'reads that start or terminate in the OPR \n') + sam <- sam[ - reads2del ,] + } + + # exclude reads that include letters that are not ACGT + # I think removing the reads that start/terminate reads above include this, but just to be safe + totnotACGT <- sapply(1:nrow(sam), function(ri) { # for each read, count the total of letters that are not ACGT + sum( ! strsplit(sam[ri,10], '')[[1]] %in% c('A', 'C', 'G', 'T')) + }) + + reads2del <- which(totnotACGT!=0) + + if (length(reads2del) != 0) { + cat('\t \t \t \t \t >>> Deleting', length(reads2del),'reads with non-ACGT nucleotide \n') + sam <- sam[ - reads2del ,] + } + + # say final number of reads we are importing + cat('\t \t \t \t \t >>> IMPORTING', nrow(sam),'READS \n') + + return(sam) + +} + + +### + +# from CIGAR of one read; get total insertion +getTotalInsertion <- function(read) { + + cigar <- read[6] + + if(length(grep(pattern='I', cigar))!=0) { + tmp <- str_extract_all(cigar, '[0-9]+I')[[1]] # extracts the I components; eg. 59I129M32I >> 59I 32I + totin <- sum(as.numeric(unlist(strsplit(tmp, '[A-Z]')))) + # split at any letter (here will be only I), so example above: 59 32 + # convert to numeric & sum + } else { + totin <- 0 + return(totin) + } +} + +### + +# from CIGAR of one read; get total deletion +getTotalDeletion <- function(read) { + + cigar <- read[6] + + if(length(grep(pattern='D', cigar))!=0) { + tmp <- str_extract_all(cigar, '[0-9]+D')[[1]] # extracts the I components; eg. 59I129M32I >> 59I 32I + totdel <- -sum(as.numeric(unlist(strsplit(tmp, '[A-Z]')))) + # split at any letter (here will be only I), so example above: 59 32 + # convert to numeric & sum & turn to negative for deletion + return(totdel) + } else { + totdel <- 0 + return(totdel) + } +} + +### + +# counts & frequencies within bins of a continuous variable (each bin = one range of values) per group + # e.g. data is number of mismatches for each read + # and 2 groups: reference / mutated + # for each group; how many reads in bin 0--10 mismatches; how many reads in bin 11-20 etc. + # both in counts and frequencies (% of total within each group) +# Note; bins represent the right boundary, e.g. a case where we have proportions, 0.1 means the bin that contains the data from 0 to 0.1 + # same in the dataframe it returns +# example usage/ freqInBins(df = mydata, datcol = 'mismatchpercentage', grpcol = 'treated', bins=seq(0, 1, by=0.1)) + +freqInBins <- function(df, datcol, grpcol, bins) { + + ngrps <- length(unique(df[,grpcol])) # number of groups + grpnms <- unique(df[,grpcol]) # group names + + cfpg <- vector(mode='list', length=ngrps) # preallocate list counts + frequencies per group + + for(i in 1:length(grpnms)) { # loop through groups + dat <- as.numeric(df[ which(df[,grpcol] == grpnms[i]) , datcol]) # data for this group (the data we need to bin) + cos <- hist(dat, breaks=bins, include.lowest=TRUE, plot=FALSE)$counts # counts + fre <- cos / sum(cos) # frequencies + + gdf <- data.frame(grp=grpnms[i], bin=bins[-1], counts=cos, freq=fre) # small dataframe for this group, two columns counts and frequencies + + # group column should be called the same as grpcol + colnames(gdf)[1] <- grpcol + + # add it to the list + cfpg[[i]] <- gdf + } + + # stick the list together and return it + fbing <- as.data.frame(rbindlist(cfpg)) # frequencies in each bin by group + return(fbing) + +} + + + + +# 1- Import what we need -------------------------------------------------- + + + # 1- Catalog of consensus OPR sequences + # OPRConsensusCatalog.csv written by generateOPRCatalog.R +cato <- read.csv(here('needleSam', 'OPRConsensusCatalog.csv')) # consensus sequence from OPRD4 up to OPRI24 + + + # 2- Meta information of samples +meta <- read.xlsx(here('AdditionalFile1.xlsx'), sheet='samples') + # make the formatting match + + # - >> NA +meta$SV[which(meta$SV=='-')] <- NA + + # special case: PDG 46345 is 5 OPRI/1 OPRD + # make a new column SV2 for it (just for the 1 OPRD) +meta <- meta %>% + mutate(SV2=NA, .after=SV) +meta[which(meta$sample==46345), 'SV2'] <- unlist(strsplit(meta[which(meta$sample==46345), 'SV'], '/'))[2] +meta[which(meta$sample==46345), 'SV'] <- unlist(strsplit(meta[which(meta$sample==46345), 'SV'], '/'))[1] + + # 2 OPRD >> OPRD2, etc. + # first lapply takes what is after the space = OPRD or OPRI + # second lapply takes what is before the space = 2, 1, ... +meta$SV <- paste0(lapply(strsplit(meta$SV, ' '), function(i) {i[2]}), + lapply(strsplit(meta$SV, ' '), function(i) {i[1]})) + # the NA above become 'NANA', put them back to NA +meta$SV[which(meta$SV=='NANA')] <- NA + + # same for SV2 +meta$SV2 <- paste0(lapply(strsplit(meta$SV2, ' '), function(i) {i[2]}), + lapply(strsplit(meta$SV2, ' '), function(i) {i[1]})) +meta$SV2[which(meta$SV2=='NANA')] <- NA + + # sample: 52331 >> pdg52331, etc. +meta$sample <- sprintf('pdg%s', meta$sample) + + # 4- Import the SAMs + # preallocate list, each element = the SAM of one sample + # 2 folders where to find the SAMs: + # one for SAMs that could not be haplotagged + # the other for SAMs that could be haplotagged +samfold <- here('controlPCR', 'filt', 'OPRtrim_sam') # folder of no-tag SAMs + +samnms <- list.files(samfold) # names of all the SAMs + +sams <- vector(mode='list', length=length(samnms)) # preallocate list that will store all the SAMs +pdgs <- 'pdg56635' +names(sams) <- pdgs # put the pdg58398 etc. as names of the elements in the list + + # gets the full paths where to find each SAM +sampaths <- list.files(samfold, full.names=TRUE) + + # fill in the list using function readSam from above +for (s in 1:length(sams)) { + cat('\t \t \t \t >>>', s, '/', length(sams), 'Reading SAM of sample', names(sams)[s], '\n') + sams[[s]] <- readSam(sampaths[s]) +} + + + + +# 2- Calculate total insertion/deletion of each read ---------------------- +# from the CIGAR; eg. 3I 2D 100M 3I 5D >> insertion = 6 bp // deletion = 5 bp + + # readSam() should have removed anything funky in HP column, but check before running below just to be sure +hpcol <- 21 +sum(unlist(lapply(sams, function(sa) { + which( substr(as.character(sa[,hpcol]), 1, 2) != 'HP') # any elements in all the HP columns that is not NA or does not start with HP +}))) == 0 + + # preallocate list of indel dataframes + # same length as sams +ies <- vector(mode='list', length=length(sams)) # ies for Insertion/dEletion dataframeS +names(ies) <- pdgs # put the pdg58398 etc. as names of the elements in the list + + # each element in the list will be a dataframe; + # column1 = sample + # column2 = haplotype (from whatshap haplotag) + # column2 = read name + # column3 = read sequence + # column3 = total insertion (in bp, as per CIGAR) + # column4 = total deletion (in bp, as per CIGAR) + +for (i in 1:length(ies)) { # for each element in the list (each sample) + + cat('\t \t \t \t >>> Format & parsing CIGARs for SAM', i, '/', length(ies), '\n') + + # preallocate the dataframe + colnms <- c('sample', 'haplotype', 'hapqual', 'read', 'samflag', 'seq', 'ins', 'del') + tmp <- as.data.frame(matrix(nrow=nrow(sams[[i]]), ncol=length(colnms))) + colnames(tmp) <- colnms + + # fill in sample name + tmp$sample <- rep(names(ies)[i], nrow(sams[[i]])) + + # fill in haplotype + tmp$haplotype <- as.numeric(substr(sams[[i]][,hpcol], 6, 6)) # simplifies the haplotype tag, from HP:i:1 / HP:i:2 to 1 / 2; will return NA if no present + + # fill in haplotype quality + tmp$hapqual <- as.numeric(substr(sams[[i]][,hpcol+1], 6, 999)) # simplifies the haplotype quality, from eg. PC:i:150 to 150 + + # fill in read names + tmp$read <- sams[[i]][,1] + + # fill in sam flags + tmp$samflag <- sams[[i]][,2] + + # fill in read sequences + tmp$seq <- sams[[i]][,10] + + # fill in total insertions + tmp$ins <- apply(sams[[i]], 1, getTotalInsertion) + + # fill in total deletions + tmp$del <- apply(sams[[i]], 1, getTotalDeletion) + + # place that sample's dataframe in the list + ies[[i]] <- tmp +} + +# turn the ies list into one big dataframe +ied <- as.data.frame(rbindlist(ies)) # for Insertion/dEletion Dataframe + +# haplotype tags: set all NA to 0 +ied$haplotype[is.na(ied$haplotype)] <- 0 + +# make sure haplotype is stored as factor +ied$haplotype <- factor(ied$haplotype, levels=c(1, 2, 0)) + +# check no duplicated read ID after pooling all samples +sum(duplicated(ied$read)) + + + + +# 5- Plot insertions/deletions for each sample ---------------------------- + +# will then assign each read to a most likely OPR based on total insertion/deletion +# should leave some space for nanopore noise + # eg. an OPRI often appears as a 23-bp insertion +# here: take the opportunity to look how much space we should leave + + # tentative thresholds +lownoise <- 6 +highnoise <- 3 + # eg. for OPRI1: ok from 24 - lownoise up to 24 + highnoise + # for example, if lownoise = 6 // highnoise = 3; considers potential OPRI1 anything from insertion of 18 bp to insertion of 27 bp + # makes sense for lownoise to be larger, as there is always a drag towards lower lengths + # (or in other words, nanopore makes more deletions errors than insertions) + +# plot an insertion + a deletion histogram for each sample +# preallocate list to store the plots +# ! one list for all deletion plots and one list for all insertion plots +ips <- vector(mode='list', length=length(pdgs)) # Insertions PlotS +names(ips) <- pdgs + +dps <- vector(mode='list', length=length(pdgs)) # Deletions PlotS +names(dps) <- pdgs + +# make a table of target insertion/deletion lengths + # eg. OPRD1 : deletion -24, etc. +# will do from OPRD4 up to OPRI24, so 4 OPRD + reference + 24 OPRI +tarl <- as.data.frame(matrix(nrow=29, ncol=2)) # target lengths +colnames(tarl) <- c('oprg', 'targetindel') # OPR genotype // target indel length +tarl$oprg <- c(sprintf('OPRD%i', 4:1) , 'reference' , sprintf('OPRI%i', 1:24)) +tarl$targetindel <- c( seq(-24*4, -24*1, 24) , 0 , seq(24*1, 24*24, 24)) # (one OPR = 24 bp) + +# first; DELETION plots +for (s in 1:length(dps)) { + + # PDG we are plotting + pd <- names(dps)[s] + + # get its OPR variant (if any) + sva <- as.character(subset(meta, sample==pd, SV)) + + # and from it the target length + target <- as.numeric(subset(tarl, oprg==sva, targetindel)) + # eg. PDG 1906 >> OPRD2 >> -48 bp + + # for that sample, count the reads with each deletion length + # can also do it automatically with geom_histogram(), but I found it leave a bar when count = 0 if computed before, which I prefer + tmp <- ied %>% + subset(sample==pd) %>% + group_by(del, haplotype) %>% + tally(name='nreads') %>% + mutate(freq=nreads/nrow(subset(ied, sample==pd))) + # above: compute frequency by dividing number of reads with each insertion length by total number of reads from that sample + + + # if sample has a OPRD: version with marker lines + # ! need to specify manually if PDG 46345 = compound homozygous 1 OPRD / 5 OPRI + if (pd =='pdg46345') { + + target <- -24 + delp <- ggplot(tmp, aes(x=del, y=freq ,colour=haplotype)) + + geom_col(fill='white', alpha=0.0, position='identity') + + scale_color_manual(values=hapcols) + + coord_cartesian(ylim=c(0,0.2), xlim=c(-250,0)) + + geom_vline(xintercept=target) + + geom_vline(xintercept=c(target-lownoise, target+lownoise), linetype=2) + + theme_minimal() + + theme( + legend.position='none' + ) + + xlab('deletion') + ylab('frequency') + + ggtitle(pd) + + } else if (!is.na(target) & target<0) { # if there is a target (i.e. sample has an OPRD) >> add the marker lines + delp <- ggplot(tmp, aes(x=del, y=freq ,colour=haplotype)) + + geom_col(fill='white', alpha=0.0, position='identity') + + scale_color_manual(values=hapcols) + + coord_cartesian(ylim=c(0,0.2), xlim=c(-250,0)) + + geom_vline(xintercept=target) + + geom_vline(xintercept=c(target-lownoise, target+lownoise), linetype=2) + + theme_minimal() + + theme( + legend.position='none' + ) + + xlab('deletion') + ylab('frequency') + + ggtitle(pd) + } else { # if not (i.e. reference or OPRI), skip the marker lines + delp <- ggplot(tmp, aes(x=del, y=freq , colour=haplotype)) + + geom_col(fill='white', alpha=0.0, position='identity') + + scale_color_manual(values=hapcols) + + coord_cartesian(ylim=c(0,0.2), xlim=c(-250,0)) + + theme_minimal() + + theme( + legend.position='none' + ) + + xlab('deletion') + ylab('frequency') + + ggtitle(pd) + } + + # in any case, add deletion plot to the list + dps[[s]] <- delp + +} + + +# second; INSERTION plots +for (s in 1:length(ips)) { + + # PDG we are plotting + pd <- names(ips)[s] + + # get its OPR variant (if any) + sva <- as.character(subset(meta, sample==pd, SV)) + + # and from it the target length + target <- as.numeric(subset(tarl, oprg==sva, targetindel)) + # eg. PDG 1906 >> OPRD2 >> -48 bp + + # for that sample, count the reads with each insertion length + # can also do it automatically with geom_histogram(), but I found it leave a bar when count = 0 if computed before, which I prefer + tmp <- ied %>% + subset(sample==pd) %>% + group_by(ins, haplotype) %>% + tally(name='nreads') %>% + mutate(freq=nreads/nrow(subset(ied, sample==pd))) + # above: compute frequency by dividing number of reads with each insertion length by total number of reads from that sample + + # if sample has a OPRI: version with marker lines + if (!is.na(target) & target>0) { + insp <- ggplot(tmp, aes(x=ins, y=freq ,colour=haplotype)) + + geom_col(fill='white', alpha=0.0, position='identity') + + scale_color_manual(values=hapcols) + + coord_cartesian(ylim=c(0,0.2), xlim=c(0,250)) + + geom_vline(xintercept=target) + + geom_vline(xintercept=c(target-lownoise, target+lownoise), linetype=2) + + theme_minimal() + + theme( + legend.position='none' + ) + + xlab('insertion') + ylab('frequency') + + ggtitle(pd) + } else { # if not (i.e. reference or OPRI), skip the marker lines + insp <- ggplot(tmp, aes(x=ins, y=freq ,colour=haplotype)) + + geom_col(fill='white', alpha=0.0, position='identity') + + scale_color_manual(values=hapcols) + + coord_cartesian(ylim=c(0,0.2), xlim=c(0,250)) + + theme_minimal() + + theme( + legend.position='none' + ) + + xlab('insertion') + ylab('frequency') + + ggtitle(pd) + } + + # in any case, add deletion plot to the list + ips[[s]] <- insp + +} + +# arrange each list of plots in a grid of one column and export + # grid of deletion plots + +delgrid <- ggarrange(plotlist=dps, ncol=1, nrow=length(dps)) +ggsave(filename=here('controlPCR', 'deletionGrid.pdf'), plot=delgrid, height=100, width=100, units='mm', useDingbats=FALSE) + +insgrid <- ggarrange(plotlist=ips, ncol=1, nrow=length(ips)) +ggsave(filename=here('controlPCR', 'insertionGrid.pdf'), plot=insgrid, height=100, width=100, units='mm', useDingbats=FALSE) + +# Note there are 3 options for the histograms above: + # position='stack' (default): each bar is a stacked barplot with proportion of each haplotype + # in a sense it is the best way to plot all the information, but intuitively when I see the tip of the bars in orange (for example), + # I imagine that there is another plot below it, which changes completely the interpretation + # position='identity': histograms for each haplotypes are effectively separated, overlayed + # position='dodge': same but the bars are a little bit shifted so there is less overlay +# I think 'identity' is the less likely to create confusion (even though it is the one with the most overlay) + + + + +# 6- Assign each read to a most likely OPR -------------------------------- +# eg. 23-bp insertion >> could be a OPRI +# below also allows OPRI + OPRD in same read, although that is unlikely + +# create the possible intervals for OPRDs +delInts <- vector(mode='list', length=4) # OPR deletion intervals +# minimum = 4 OPRD = - 24 * 4 +# maximum = 1 OPRD = -24 * 1 +delOpr <- seq(-24*4, -24*1, 24) +for (o in 1:length(delOpr)) { + delInts[[o]] <- (delOpr[o] - lownoise) : (delOpr[o] + highnoise) +} +names(delInts) <- sprintf('OPRD%i', 4:1) + +# create the possible intervals for OPRIs +inInts <- vector(mode='list', length=24) # OPR insertion intervals +# minimum = 1 OPRI = 24 * 1 +# maximum = 24 OPRI = 24 * 24 +inOpr <- seq(24*1, 24*24, 24) +for (o in 1:length(inOpr)) { + inInts[[o]] <- (inOpr[o] - lownoise) : (inOpr[o] + highnoise) +} +names(inInts) <- sprintf('OPRI%i', 1:24) + +# create the possible interval for reference + # reference interval is a bit different as will overlap deletions/insertions + # i.e. centered around 0, - lownoise / + highnoise +refInt <- (0-lownoise):(0+highnoise) + +# given one total insertion (in bp), check if belongs to one OPRI interval + # eg. +23 bp >> return OPRI1 +checkOPRI <- function(totin) { + + check <- unlist(lapply(inInts, function(int){totin %in% int})) + + if (length(which(check==TRUE))==0){ + return(NA) + } else( + return(names(which(check) == TRUE)) + ) +} + +# given one total deletion (in bp), check if belongs to one OPRD interval +# eg. -23 bp >> return OPRD1 +checkOPRD <- function(totdel) { + + check <- unlist(lapply(delInts, function(int){totdel %in% int})) + + if (length(which(check==TRUE))==0){ + return(NA) + } else( + return(names(which(check) == TRUE)) + ) +} + +# given both total deletion / total insertion, check if it should be categorised as reference + # eg. -3 bp >> return reference + # ! flipping around here: functions above are meant to be applied to all column; checkRef is meant to be apply to each row of ied + # (because need both totdel & totins for each read) +checkRef <- function(read) { # read = row of ied + + totdel <- read['del'] + totins <- read['ins'] + + # del and ins should be both in interval + # eg. -5 del / +1 ins >> reference + # eg. -12 del / +2 ins >> NA (in this case read will not have a category as deletion too small for an OPRD1) + check <- (totdel %in% refInt) & (totdel %in% refInt) # check will be Logical, are both totdel / totins in Ref interval + + if (check) { + read['del'] <- 'reference' + read['ins'] <- 'reference' + return(read) + } else { + return(read) + } +} + +# now assign reads to possible OPR mutations +ied$opri <- sapply(ied$ins, checkOPRI) +ied$oprd <- sapply(ied$del, checkOPRD) + +# put reads that were not assigned to an OPRI and/or an OPRD in either 'reference' or 'unassigned' + # 'reference' = total insertion & total deletion are in reference length interval (i.e. no or small insertion + no or small deletion) + # 'unassigned' = none of total insertion or total deletion are in any interval (so anything falling between the cracks, eg. a 10 bp insertion) +# create a new column for these categories (prevents from plotting same reads in different plots below) +ied$othercategory <- NA +ied[which((ied$ins %in% refInt) & (ied$del %in% refInt)) , 'othercategory'] <- 'reference' +# explicitly call all the leftover reads 'unassigned'; leftover = + # do not have an OPRD + # do not have an OPRI + # are NA for othercategory (i.e. were not categorised as reference above) +ied[which(is.na(ied$opri) & is.na(ied$oprd) & is.na(ied$othercategory)) , 'othercategory'] <- 'unassigned' + +# Note1; reads categorised as 'reference' or 'unassigned' will always be OPRI NA / OPRD NA +# Note2; it is a bit of a pain to keep 3 columns when really each read should be in a single category + # (i.e. has an OPRI OR has OPRD OR is reference OR is unassigned) + # the only advantage is to leave the opportunity for a single read to be both OPRD & OPRI + # which are (hopefully) cases which will go away when aligning later + +# Check + # that means all reads should be in at least one category + # i.e. all three columns cannot be NA at once +subset(ied, is.na(opri) & is.na(oprd) & is.na(othercategory)) + + + + +### ... + + + + +# Check strand directions ------------------------------------------------- + +# check nothing else than 0 (= forward) or 16 (= reverse complement) in samflag column +which(ied$samflag!=0 & ied$samflag!=16) # ok + +# if yes -- replace all 0 to +, all 16 to - +ied[which(ied$samflag==0), 'samflag'] <- '+' +ied[which(ied$samflag==16), 'samflag'] <- '-' + +# check all +/- now +which(ied$samflag!='+' & ied$samflag!='-') +# ok + +# change column name to strand +colnames(ied)[which(colnames(ied)=='samflag')] <- 'strand' + +# quick sanity checks with strand direction +strandcount <- ied %>% + group_by(strand) %>% + tally(name='count') %>% + mutate(prop=count/nrow(ied)) + +strandPro <- ggplot(strandcount, aes(x=strand, y=prop)) + + geom_col() + + theme_minimal() + + xlab('proportion of reads') + ylab('strand') +strandPro +ggsave(here('controlPCR', 'strand.pdf'), strandPro, width=100, height=100, units='mm') + +# add a dummy column +strandcount$dummy <- factor(1) + +# same but stack +strandProStack <- ggplot(strandcount, aes(x=dummy, y=prop, fill=strand)) + + geom_col() + + theme_minimal() + + xlab('proportion of reads') +strandProStack +ggsave(here('controlPCR', 'strandProStack.pdf'), strandProStack, width=100, height=100, units='mm') + +# ... + + + +# 8- Alignment to consensus OPR sequences --------------------------------- + +# for example, say a read has an insertion of 92 bp >> it could be a OPRI4 +# how can we measure how convincing it is? +# we will align to a consensus sequence of what an OPRI4 looks like +# this makes use of the consensus R sequence written by Simon, which uses flexible nucleotides (eg. Y = C or T) +# >> see OPRconsensus.xlsx / generateOPRCatalog.R / OPRConsensusCatalog.xlsx for more information + +# previously: was trying alignment to published OPR sequences + # but there is some logic to which nucleotides can change, so better to define a consensus sequence + # advantage: it includes more possible OPRs (OPR sequences that are probably out there but were never detected or published) + + +# function msaConsensusFlexible takes an alignment and outputs a corrected consensus sequence + # ! msa support alignment with flexible nucleotides, see https://github.com/UBod/msa/issues/12 + # but eg. G vs A returns R; which is correct but not what I want here + # I want to leave flexibility only if the reference leaves that option open + # where eg. Y vs T returns Y +# build look-up table for flexible nucleotides +fnu <- c('R', 'Y', 'S', 'W', 'K', 'M', 'B', 'D', 'H', 'V', 'N') # flexible nucleotides +lut <- as.data.frame(matrix(nrow=4, ncol=length(fnu))) +colnames(lut) <- fnu +lut$R[1:2] <- c('A', 'G') +lut$Y[1:2] <- c('C', 'T') +lut$S[1:2] <- c('G', 'C') +lut$W[1:2] <- c('A', 'T') +lut$K[1:2] <- c('G', 'T') +lut$M[1:2] <- c('A', 'C') +lut$B[1:3] <- c('C', 'G', 'T') +lut$D[1:3] <- c('A', 'G', 'T') +lut$H[1:3] <- c('A', 'C', 'T') +lut$V[1:3] <- c('A', 'C', 'G') +lut$N[1:4] <- c('A', 'C', 'G', 'T') + +# msaConsensusFlexible + # use instead of msaConsensusSequence, will return the consensus sequence of an alignment, but + # will replace ? in the consensus sequence which were thrown because of the presence of a flexible nucleotide, where the alignment was fine (eg. Y vs T) + # ! Note; it assumes alignment one-to-one and only one of the sequence (typically the reference) allows flexible nucleotides +msaConsensusFlexible <- function (alignment){ + conm <- consensusMatrix(alignment) + cons <- msaConsensusSequence(alignment) + + sapply(1:ncol(conm), function(pos) { # for each position of the alignment + + al <- conm[,pos] # get the alignment matrix at that position + # count number of flexible nucleotides at that position + nfnu <- sum(al[which(names(al) %in% fnu)]) + + if (nfnu==0) { # if no flexible nucleotide at that position, do nothing + return(NULL) + } + + if (nfnu>0) { # if any flexible nucleotide at that position + # get the flexible nucleotide + f <- names(which(al[which(names(al) %in% fnu)] > 0)) + + # get the standard nucleotide + s <- names(which(al[which(!names(al) %in% fnu)] > 0)) + + # is the alignment valid? Check in the look-up table; eg. T vs Y is ok + if (!s %in% lut[,f]) { # if not -- do NOT modify the consensus sequence at that position (should leave ?) + return(NULL) + } + + else if (s %in% lut[,f]) { # if yes -- modify the consensus sequence at that position (should put the flexible nucleotide instead of the ?) + substr(cons, pos, pos) <<- f + } + } + + }) + + return(cons) + +} + + +# function alignCon_NumMis: + # takes a query DNA sequence (i.e. possible somatic mutation) + # looks at the possible OPRD/OPRI for that read + # takes consensus DNA sequence from the catalog of OPRs (by allele) + # try aligning to the consensus sequence, gets number of mismatches + # reports the number of mismatches vs consensus +alignCon_NumMis <- function(query, allele) { + # eg. alignRef_NumMis('CGAAATGC', 'OPRD1'), i.e. try aligning CGAAATGC to the consensus OPRD1 sequence and tell me number of mismatches + # can also be alignRef_NumMis('CGAAATGC', 'reference') + + if( is.na(allele) | allele=='unassigned') { # if allele is NA (eg. a 8OPRI read will usually have NA in oprd column; all unassigned reads are opri/oprd NA; etc.) + return(NA) + } + + if(! allele %in% cato$genotype) { # check the allele is in catalog (I think should always be ok as catalog covers all possible cases) + stop('\t \t \t \t >>> Allele', allele, ' was not found in catalog \n') + } + + + # 1- take the consensus sequence (used as reference) + ref <- as.character(subset(cato, genotype==allele, consensusseq)) + + # 2- align query to that reference + ali <- msa(c(ref, query), type='dna', method='ClustalW') + + # 3- correct the consensus sequence to allow flexible nucleotides + # using msaConsensusFlexible() + con <- msaConsensusFlexible(ali) + + # 4- count number of mismatches (?) + nmis <- str_count(con, '\\?') + + # return that + return(nmis) + +} + +# sanity checks + # align reference OPR to the consensus sequence +alignCon_NumMis('CCTCAGGGCGGTGGTGGCTGGGGGCAGCCTCATGGTGGTGGCTGGGGGCAGCCTCATGGTGGTGGCTGGGGGCAGCCCCATGGTGGTGGCTGGGGACAGCCTCATGGTGGTGGCTGGGGTCAA', + 'reference') +# gives 0 mismatch + + # check eg. G vs A should NOT return R; only edit consensus if reference leaves the option open +alitest <- msa(c('CYGTK', 'CTAAT'), type='dna', method='ClustalW') # should return C Y ? ? K +msaConsensusFlexible(alitest) # ok + + +tic('\t \t \t \t Aligning reads took... \n') + +# align all possible OPRI reads to their consensus sequence +opri_mis <- sapply(1:nrow(ied), function(ri){ # ri = read index; opri_mats = OPRI mismatches + # Note; will be one element per row of ied, can add to ied as it + cat('\t \t \t \t >>> Read', ri, 'out of', nrow(ied), '\n') + + readseq <- as.character(ied[ri, 'seq']) # read sequence + oprgeno <- as.character(ied[ri, 'opri']) # possible OPR allele + + alignCon_NumMis(readseq, oprgeno) +}) + +# put the results in ied +ied$opri_nummis <- opri_mis + + + +# align all possible OPRD reads to their consensus sequence +oprd_mis <- sapply(1:nrow(ied), function(ri){ # ri = read index; oprd_mis = OPRD mismatches + cat('\t \t \t \t >>> Read', ri, 'out of', nrow(ied), '\n') + + readseq <- as.character(ied[ri, 'seq']) # read sequence + oprgeno <- as.character(ied[ri, 'oprd']) # possible OPR genotype + + alignCon_NumMis(readseq, oprgeno) +}) + +# put the results in ied +ied$oprd_nummis <- oprd_mis + + + +# align reference reads to the consensus sequence +ref_mis <- sapply(1:nrow(ied), function(ri){ # ri = read index; ref_mis = reference mismatches + cat('\t \t \t \t >>> Read', ri, 'out of', nrow(ied), '\n') + + readseq <- as.character(ied[ri, 'seq']) # read sequence + oprgeno <- as.character(ied[ri, 'othercategory']) # take what is othercategory column as allele + # Note alignCon_NumMis takes care of 'unassigned' already, i.e. returns NA (as there is nothing to align to) + + alignCon_NumMis(readseq, oprgeno) +}) + +# put the results in ied +ied$reference_nummis <- ref_mis + + +toc() + + + + +# 9- Threshold for maximum number of mismatches? -------------------------- +# what is a good threshold for maximum number of mismatches? +# eg. if 25% of the nucleotides in one read do not match the consensus OPR sequence, might not be so convincing +# >> look at the 'positive control' distribution of number of mismatches + # eg. take sample genotyped as OPRD2 by Sanger + # take all the reads that are consistent with an OPRD2 + # and look at their number of mismatches with OPRD2 consensus sequence + +# add samples metadata +ied <- left_join(x=ied, y=meta, by='sample') + # we do not need the colour column +ied$colour <- NULL + +# plot mismatches plot +# list to store mismatches plots +# will basically do one list for each copy of the genome, i.e. + # first list = all the SVs or reference for the samples w/o SV + # second list = reference for the samples that have a SV / OPRD1 for the compound homozygous sample + +# List 1 +misPlots1 <- vector(mode='list', length=length(pdgs)) +names(misPlots1) <- pdgs + +for (s in 1:length(pdgs)) { + + # get the PDG we are plotting + pdg <- pdgs[[s]] + + # get its Sanger genotype + sang <- as.character(unique(subset(ied, sample==pdg, SV))) + + + # if Sanger genotype is NA (example sCJD case) + if (is.na(sang)) { # then plot the mismatches vs reference + + # then it means its genotype is reference + sang <- 'reference' + + tmp <- subset(ied, sample==pdg & othercategory==sang) # subset of ied for plot + misplot <- ggplot(tmp, aes(reference_nummis, after_stat(density))) + # mismatches plot + geom_histogram(binwidth=1) + + theme_minimal() + + coord_cartesian(xlim=c(0,100), ylim=c(0, 0.3)) + + labs(title=pdg, + subtitle=sang) + misPlots1[[s]] <- misplot # add it to the list + + + # if Sanger genotype is an insertion... + } else if (substr(sang, 1, 4) == 'OPRI') { + + tmp <- subset(ied, sample==pdg & opri==sang) # subset of ied for plot + misplot <- ggplot(tmp, aes(opri_nummis, after_stat(density))) + # mismatches plot + geom_histogram(binwidth=1) + + theme_minimal() + + coord_cartesian(xlim=c(0,100), ylim=c(0, 0.3)) + + labs(title=pdg, + subtitle=sang) + misPlots1[[s]] <- misplot # add it to the list + + # if Sanger genotype is a deletion... + } else if (substr(sang, 1, 4) == 'OPRD') { + + tmp <- subset(ied, sample==pdg & oprd==sang) # subset of ied for plot + misplot <- ggplot(tmp, aes(oprd_nummis, after_stat(density))) + # mismatches plot + geom_histogram(binwidth=1) + + theme_minimal() + + coord_cartesian(xlim=c(0,100), ylim=c(0, 0.3)) + + labs(title=pdg, + subtitle=sang) + misPlots1[[s]] <- misplot # add it to the list + } +} + +# List 2 +misPlots2 <- vector(mode='list', length=length(pdgs)) +names(misPlots2) <- pdgs + +for (s in 1:length(pdgs)) { + + # get the PDG we are plotting + pdg <- pdgs[[s]] + + # get its first Sanger genotype + sang <- as.character(unique(subset(ied, sample==pdg, SV))) + + if (is.na(sang)) { # if its first Sanger genotype is NA, we already plotted the reference reads above + # so do not repeat the plot but instead plot an empty plot to fill the list + misplot <- ggplot() + + theme_void() + + labs(title=pdg) + misPlots2[[s]] <- misplot # add it to the list + + # if first Sanger genotype is not NA, then we should plot the reference reads now + # (or the 1 OPRD reads for the compound homozygous; will be in SV2 column) + } else if(!is.na(sang)) { + + sang2 <- as.character(unique(subset(ied, sample==pdg, SV2))) # look at SV2 column, the only one not NA is the compound homozygous + + if(is.na(sang2)) { + # then it means we should plot the reference reads + sang2 <- 'reference' + + tmp <- subset(ied, sample==pdg & othercategory==sang2) # subset of ied for plot + misplot <- ggplot(tmp, aes(reference_nummis, after_stat(density))) + # mismatches plot + geom_histogram(binwidth=1) + + theme_minimal() + + coord_cartesian(xlim=c(0,100), ylim=c(0, 0.3)) + + labs(title=pdg, + subtitle=sang2) + misPlots2[[s]] <- misplot # add it to the list + + # if not NA, i.e. we are dealing with the compound homozygous; so it will be 1 OPRD + } else if (!is.na(sang2)) { + if(sang2!='OPRD1') stop('\t \t \t \t >>> Something unexpected with the compound homozygous sample \n') # check that is correct + + tmp <- subset(ied, sample==pdg & oprd==sang2) # subset of ied for plot + misplot <- ggplot(tmp, aes(oprd_nummis, after_stat(density))) + # mismatches plot + geom_histogram(binwidth=1) + + theme_minimal() + + coord_cartesian(xlim=c(0,100), ylim=c(0, 0.3)) + + labs(title=pdg, + subtitle=sang2) + misPlots2[[s]] <- misplot # add it to the list + } + + } +} + +# interleave the two lists +orderindex <- order(c(seq_along(misPlots1), seq_along(misPlots2))) # gives 1, 26, 2, 27, etc; so can concatenate both lists then order them +misPlots <- (c(misPlots1,misPlots2))[orderindex] + +# arrange the interleaved list in a grid +misGrid <- ggarrange(plotlist=misPlots, nrow=length(pdgs), ncol=2) # should produce each row = one sample +ggsave(filename=here('controlPCR', 'mismatches_vsconsensus.pdf'), misGrid, height=200, width=100, units='mm', limitsize=FALSE) + +# there is some effect of length on number of mismatches (expectedly); i.e. longer reads (eg. OPRI8) = more mismatches +# I think need to have a flexible threshold based on % error by nucleotide + +# below: look at effect of length on number of mismatches + +# for all 'expected genotype' reads, plot number of mismatches vs read length + # add a read length column +ied$read_length <- nchar(ied$seq) + +# subset we are interested in = all 'true' reads + # = all reference reads (except for compound homozygous) + # + all reads that match Sanger genotype (! 2 Sanger genotypes for compound homozygous) + +# will add a 'true read' column and then subset based on that +ied$trueread <- NA + + # all reference reads, except for PDG 46345 +ied[which(ied$sample != 'pdg46345' & ied$othercategory == 'reference'), 'trueread'] <- TRUE + + # all reads which have an OPRI that match their SV +ied[which(ied$opri == ied$SV), 'trueread'] <- TRUE + + # all reads which have an OPRI that match their SV2 (will only apply to PDG 46345) +ied[which(ied$opri == ied$SV2), 'trueread'] <- TRUE + + # all reads which have an OPRD that match their SV +ied[which(ied$oprd == ied$SV), 'trueread'] <- TRUE + + # all reads which have an OPRD that match their SV2 (will only apply to PDG 46345) +ied[which(ied$oprd == ied$SV2), 'trueread'] <- TRUE + + # total number of 'true reads' +sum(ied$trueread, na.rm=TRUE) +sum(ied$trueread, na.rm=TRUE) / nrow(ied) + + # will put FALSE for all unassigned reads +ied[which(ied$othercategory == 'unassigned'), 'trueread'] <- FALSE + + # how many NA left +sum((is.na(ied$trueread))) + +# looks correct, essentially all reads left NA have a potential somatic mutation + # mismatch threshold will say if convincing or not, though + + # put FALSE for these reads +ied[which(is.na(ied$trueread)), 'trueread'] <- FALSE + + # check no more NA in trueread +sum(is.na(ied$trueread)) + + +# subset ied to keep only true reads +iedTrue <- subset(ied, + trueread) + + +# few checks +# there should not be any unassigned reads +subset(iedTrue, othercategory=='unassigned') +# there should not be any reads from pdg46345 that is reference +subset(iedTrue, sample=='pdg46345' & othercategory=='reference') +# there should not be any eg. 3 OPRI (as no sample has that as its Sanger genotype) +subset(iedTrue, opri=='OPRI3') +subset(iedTrue, opri=='OPRD3') + +# looks good + # ! number of mismatches are spread out between 3 columns + # need to collapse both columns in one + # first; check there is no case where both OPRD and OPRI are not NA +subset(iedTrue, !is.na(opri_nummis) & !is.na(oprd_nummis)) # check okay to delete... If only a few and one of opri_nummis or oprd_nummis is high +inds2del <- which(!is.na(iedTrue$opri_nummis) & !is.na(iedTrue$oprd_nummis)) + +if (length(inds2del) != 0) { + iedTrue <- iedTrue[ - inds2del , ] +} + +# quick sanity checks +subset(iedTrue, !is.na(opri) & is.na(opri_nummis)) +subset(iedTrue, is.na(opri) & !is.na(opri_nummis)) + +subset(iedTrue, !is.na(oprd) & is.na(oprd_nummis)) +subset(iedTrue, is.na(oprd) & !is.na(oprd_nummis)) + +identical(which(is.na(iedTrue$opri)) , which(is.na(iedTrue$opri_nummis))) +identical(which(is.na(iedTrue$oprd)) , which(is.na(iedTrue$oprd_nummis))) + +# also, wherever read is reference, it is NA for both opri/oprd +subset(iedTrue, !is.na(reference_nummis) & (!is.na(opri) | !is.na(oprd))) + +# or in summary, for each row there should only be one of OPRI/OPRD/othercategory that is not NA +checkNa <- apply(iedTrue, 1, function(re) { + totna <- as.numeric(!is.na(re['opri_nummis'])) + as.numeric(!is.na(re['oprd_nummis'])) + as.numeric(!is.na(re['reference_nummis'])) + return(totna) +}) +# should always be 1 +which(checkNa != 1) +# ok so we can collapse into one column + +# now to collapse both columns in one: +iedTrue$true_nummis <- NA # preallocate the column + +# fill in the OPRI +iedTrue$true_nummis [which(!is.na(iedTrue$opri_nummis))] <- iedTrue$opri_nummis[which(!is.na(iedTrue$opri_nummis))] +iedTrue$true_nummis [which(!is.na(iedTrue$oprd_nummis))] <- iedTrue$oprd_nummis[which(!is.na(iedTrue$oprd_nummis))] +iedTrue$true_nummis [which(!is.na(iedTrue$reference_nummis))] <- iedTrue$reference_nummis[which(!is.na(iedTrue$reference_nummis))] + # left which() gives the indices to fill in / right which() gets all the non-NA OPRI + +# there should not be any NA left +sum(is.na(iedTrue$true_nummis)) # ok + +# let's put this column back into ied, will make life easier + # can simply left_join by read ID, it is safe as no duplicated read + # check to be safe +sum(duplicated(ied$read)) +tmp <- select(iedTrue, read, true_nummis) # keep only read/true_nummis columns +ied <- left_join(x=ied, y=tmp, by='read') + +# easy check: all trueread TRUE should have a true_nummis +subset(ied, + trueread & is.na(true_nummis)) + # few reads, which are the one which have both an OPRI and an OPRD (see above), it is fine we can leave them there + +# or in other words, all FALSE trueread should be NA true_nummis +subset(ied, + !trueread & !is.na(true_nummis)) +# ok + +# plot read length vs number of mismatches + # can do from ied now; all not 'true read' will have NA for true_nummis and will not be plotted +lengthVsMis <- ggplot(ied, aes(x=read_length, y=true_nummis)) + + geom_point() + + theme_minimal() + + coord_cartesian(xlim=c(0, 350)) +lengthVsMis +ggsave(filename=here('controlPCR', 'lengthVsMis.pdf'), lengthVsMis, width=300, height=300, units='mm') + +# for any read length, most reads are with low number of mismatches which is good news +# however, there is a clear effect of read length as expected + # it increases the variability of number of mismatches & the number of reads with many mismatches + +# perhaps clearer if plotting average mismatch for each read length +meanMisbyLength <- ied %>% + group_by(read_length) %>% + summarise(meanMis=mean(true_nummis, na.rm=TRUE)) + +meanMisbyLengthPlot <- ggplot(meanMisbyLength, aes(x=read_length, y=meanMis)) + + geom_point() + + theme_minimal() +meanMisbyLengthPlot +ggsave(filename=here('controlPCR', 'meanMisbyLength.pdf'), meanMisbyLengthPlot, width=300, height=300, units='mm') +# interestingly it makes like a chainsaw pattern +# I think it is simpl because reads tend to have lowest number of mismatches when their length match the target + # eg. reference = 123 bp, reads that are exactly 123 bp are more likely to have low number of mismatches + # a reference read that is eg. 118 bp will necessarily have at least 6 mismatches +# correlation read_length vs number of mismatches +cor(ied$read_length, ied$true_nummis, use='complete.obs') + +# Normalise number of mismatches by doing % mismatch by nucleotide + # compute % mismatches by nucleotide + # simply need to divide mismatches by read_length +ied$true_misbp <- ied$true_nummis / ied$read_length # true read, mismatch by bp + +# how does it look + # mean / sd will give us an idea of the appropriate threshold +mismatchByNucleotide <- ggplot(ied, aes(true_misbp, after_stat(density))) + + geom_histogram(binwidth=0.01) + + geom_vline(xintercept=mean(ied$true_misbp, na.rm=TRUE), linetype=1) + + geom_vline(xintercept=mean(ied$true_misbp, na.rm=TRUE) + sd(ied$true_misbp, na.rm=TRUE), linetype=2) + + theme_minimal() +mismatchByNucleotide +ggsave(filename=here('controlPCR', 'mismatchByNucleotide.pdf'), mismatchByNucleotide, width=100, height=100, units='mm') + +# >> I am happy with mean + 1*sd as threshold 'mismatch by nucleotide' +thrMis <- mean(ied$true_misbp, na.rm=TRUE) + sd(ied$true_misbp, na.rm=TRUE) +cat('\t \t \t \t >>> Maximum mismatches allowed vs consensus sequence =', round(thrMis*100, 2), '% of the read length \n') +cat('\t \t \t \t \t or in other words,', round(100-thrMis*100, 2), '% of the read has to align correctly to its consensus sequence \n') + +# controlPCR: I think should use same threshold as before +thrMis <- 0.058 + + + + +# 10- Filter by maximum number of mismatches ------------------------------- + +# thrMis is the maximum number of mismatches by nucleotide +# compute the maximum number of mismatches authorised for each read + # i.e. read_length * thrMis +ied$authMis <- round(ied$read_length * thrMis) # number of mismatches authorised + +# how many cases are there where one read is both OPRI + OPRD? +nrow(subset(ied, !is.na(opri) & !is.na(oprd))) + +# now add a TRUE/FALSE to the reads that are below + # because of above, will add 2 columns, opri_pass and oprd_pass +ied$opri_pass <- ied$opri_nummis < ied$authMis +ied$oprd_pass <- ied$oprd_nummis < ied$authMis + +# ! for PDG 46345 (compound homozygous OPRD1/OPRI5), should consider reference reads as possible somatic mutations +# will simply add a column ref_pass for all; same as above +ied$ref_pass <- ied$reference_nummis < ied$authMis + +# check it does what I expect to the PDG 46345 reads +subset(ied, sample=='pdg46345' & othercategory=='reference') + + +# can also compute % mismatch by nucleotide for each read + # I am finding it less intuitive, but it has the advantage to be more flexible later as can be used with another threshold later + # same as above, we need to do it in 3 columns +ied$opri_misbp <- ied$opri_nummis / ied$read_length # mismatches by bp for all OPRI reads +ied$oprd_misbp <- ied$oprd_nummis / ied$read_length # mismatches by bp for all OPRD reads +ied$ref_misbp <- ied$reference_nummis / ied$read_length # mismatches by bp for all reference reads + + + + +# write the database ------------------------------------------------------ +# (as alignments take a while) +# and we will start exploring it in needleSam_exploration.R + +# format a bit better ied + +# remove metadata information, only keep read-level info +cols2remove <- c('individual', 'cohortID', 'cohort', 'gDNA_tissue', 'prion_disease', + 'SV', 'SV2', 'codon129', 'otherSNVs', 'flowcell', + 'gender', 'birth_date', 'sample_date', 'death_date', 'death_age', + 'onset_age', 'age_atsample', 'MRC_t0', 'MRC_intersect', 'MRC_slope') +cols2remove <- match(cols2remove, colnames(ied)) + +ied <- ied[, -cols2remove] + +# arrange columns order +colsorder <- c('sample', 'read', 'seq', 'read_length', 'strand', 'haplotype', 'hapqual', + 'ins', 'del', 'opri', 'oprd', 'othercategory', 'opri_nummis', 'oprd_nummis', + 'reference_nummis', 'trueread', 'true_nummis', 'true_misbp', 'authMis', + 'opri_pass', 'oprd_pass', 'ref_pass', 'opri_misbp', 'oprd_misbp', 'ref_misbp') +length(colsorder) == ncol(ied) +colsorder <- match(colsorder, colnames(ied)) +ied <- ied[, colsorder] + +# write the database +write.csv(ied, file=here('controlPCR', 'conPCR_allOPRreads.csv'), row.names=FALSE) + +# >>> move to needleSam_exploration.R \ No newline at end of file diff --git a/controlPCR/conPCR_needleSam_exploration.R b/controlPCR/conPCR_needleSam_exploration.R new file mode 100644 index 0000000..5812aee --- /dev/null +++ b/controlPCR/conPCR_needleSam_exploration.R @@ -0,0 +1,473 @@ +# Note, below is all taken directly from needleSam_exploration.R +# here, applied to the control PCR on sample #56635 +# will do as little modifications as possible, so will look convoluted as original script is applied on all the samples + +# after needleSam.R + # needleSam.R creates the dataset allOPRreads.csv + # needleSam_exploration.R: exploring the dataset for possible OPR somatic mutations + +exportOrNo <- FALSE # Do you want to export the plots (useful to put FALSE when just want to load everything) + +# packages ---------------------------------------------------------------- + +library(here) +library(tidyr) +library(dplyr) +library(ggplot2) +library(openxlsx) +library(ggbeeswarm) +library(ggpubr) + + + +# small functions --------------------------------------------------------- + +# function to pool columns from a dataframe into one column + # ! assumes that each row, there is only one element from the columns to pool which is not NA + # eg. at row 5, the columns we want to pool are NA, 9, NA >> gives 9 + # but if 2, 9, NA >> Error! (as more than one element) + +# usage example; poolColumns(df, c('col2', 'col5')) +poolColumns <- function(dataframe, vectorOfColNames) { + apply(dataframe, 1, function(row) { + tmp <- as.vector(unlist(c(row[vectorOfColNames]))) # concatenate the columns we need to pool at this row + # check there is only one not NA + if (sum(!is.na(tmp)) != 1) stop ('\t \t \t \t >>> Error: One or more rows has more than one element in the columns to be pooled \n') + # if ok, remove the NA and we are left with a single element + return(tmp[!is.na(tmp)]) # return for within the apply + }) +} + +### + +# counts & frequencies within bins of a continuous variable (each bin = one range of values) per group +# e.g. data is number of mismatches for each read +# and 2 groups: reference / mutated +# for each group; how many reads in bin 0--10 mismatches; how many reads in bin 11-20 etc. +# both in counts and frequencies (% of total within each group) +# Note; bins represent the right boundary, e.g. a case where we have proportions, 0.1 means the bin that contains the data from 0 to 0.1 +# same in the dataframe it returns +# example usage/ freqInBins(df = mydata, datcol = 'mismatchpercentage', grpcol = 'treated', bins=seq(0, 1, by=0.1)) +# by default grpcol = NA, meaning it does do it by any group, just takes all the data in column datcol +freqInBins <- function(df, datcol, grpcol=NA, bins) { + + ### + # if no grouping + if (is.na(grpcol)) { + dat <- as.numeric(df[, datcol]) # data we need to bin + cos <- hist(dat, breaks=bins, include.lowest=TRUE, plot=FALSE)$counts # counts + fre <- cos / sum(cos) # frequencies + gdf <- data.frame(bin=bins[-1], counts=cos, freq=fre) # small dataframe for this group, two columns counts and frequencies + + return(gdf) + + } + + ### + # if grouping + + else { + + ngrps <- length(unique(df[,grpcol])) # number of groups + grpnms <- unique(df[,grpcol]) # group names + + cfpg <- vector(mode='list', length=ngrps) # preallocate list counts + frequencies per group + + for(i in 1:length(grpnms)) { # loop through groups + dat <- as.numeric(df[ which(df[,grpcol] == grpnms[i]) , datcol]) # data for this group (the data we need to bin) + cos <- hist(dat, breaks=bins, include.lowest=TRUE, plot=FALSE)$counts # counts + fre <- cos / sum(cos) # frequencies + + gdf <- data.frame(grp=grpnms[i], bin=bins[-1], counts=cos, freq=fre) # small dataframe for this group, two columns counts and frequencies + + # group column should be called the same as grpcol + colnames(gdf)[1] <- grpcol + + # add it to the list + cfpg[[i]] <- gdf + } + + # stick the list together and return it + fbing <- as.data.frame(rbindlist(cfpg)) # frequencies in each bin by group + return(fbing) + } + +} + + +# plot colours ------------------------------------------------------------ + +# somatic call TRUE/FALSE +somcols <- c('#f1876b', '#B3BDC4') + +# strand + # will use same colours as IGV + # forward = pink; reverse = blue +strcols <- c('#ebb0af', '#aeafd8') # ! Forward, Reverse + +# haplotypes +hapcols <- c('#f1876b', '#4D4D4D', '#B3BDC4') # ! 1, 2, 0 + +# cohorts + # inherited = yellow + # sCJD = khaki + # control = grey +cohcols <- c('#fcb505', '#78ac63', '#B3BDC4') + + + + +# import ------------------------------------------------------------------ + +# all the reads +ied <- read.csv(here('controlPCR', 'conPCR_allOPRreads.csv')) + +# sample metadata +meta <- read.xlsx(here('AdditionalFile1.xlsx'), sheet='samples') + +# format meta as in needleSam.R + # - >> NA +meta$SV[which(meta$SV=='-')] <- NA + + # special case: PDG 46345 is 5 OPRI/1 OPRD + # make a new column SV2 for it (just for the 1 OPRD) +meta <- meta %>% + mutate(SV2=NA, .after=SV) +meta[which(meta$sample==46345), 'SV2'] <- unlist(strsplit(meta[which(meta$sample==46345), 'SV'], '/'))[2] +meta[which(meta$sample==46345), 'SV'] <- unlist(strsplit(meta[which(meta$sample==46345), 'SV'], '/'))[1] + + # 2 OPRD >> OPRD2, etc. + # first lapply takes what is after the space = OPRD or OPRI + # second lapply takes what is before the space = 2, 1, ... +meta$SV <- paste0(lapply(strsplit(meta$SV, ' '), function(i) {i[2]}), + lapply(strsplit(meta$SV, ' '), function(i) {i[1]})) + # the NA above become 'NANA', put them back to NA +meta$SV[which(meta$SV=='NANA')] <- NA + + # same for SV2 +meta$SV2 <- paste0(lapply(strsplit(meta$SV2, ' '), function(i) {i[2]}), + lapply(strsplit(meta$SV2, ' '), function(i) {i[1]})) +meta$SV2[which(meta$SV2=='NANA')] <- NA + + # sample: 52331 >> pdg52331, etc. +meta$sample <- sprintf('pdg%s', meta$sample) + + +# haplotype phasing metadata + # eg. how many SNVs available for haplotagging +hpmeta <- read.xlsx(here('AdditionalFile1.xlsx'), sheet='haplotypephasing') + # sample: 52331 >> pdg52331, etc. +hpmeta$sample <- sprintf('pdg%s', hpmeta$sample) + + # from this: + # pdgs of samples that we could haplotag +pdgs_tag <- as.character(unlist(subset(hpmeta, haplotagged, sample))) + # pdgs of samples we could not haplotag +pdgs_notag <- as.character(unlist(subset(hpmeta, !haplotagged, sample))) + +# sequencing results summary +seqmeta <- read.xlsx(here('AdditionalFile1.xlsx'), sheet='sequencing_summary') +# sample: 52331 >> pdg52331, etc. +seqmeta$sample <- sprintf('pdg%s', seqmeta$sample) + +# we will also need all pdgs +pdgs <- meta$sample +# do not take the ones we do not have loaded (only applies if running script on subset of samples) +pdgs <- intersect(unique(ied$sample), pdgs) + + + + +# add sample info to ied for simplicity ----------------------------------- + +ied <- left_join(ied, meta, by='sample') + +ied <- hpmeta %>% + select('sample', 'haplotagged', 'genebody_heterozygousSNVs') %>% + left_join(ied, ., by='sample') + +ied <- seqmeta %>% + select('sample', 'genebody_coverage', 'regulatoryregion_coverage') %>% + left_join(ied, ., by='sample') + + + + +# Possible somatic mutations: approach 1 ---------------------------------- + +# there is no read that has both an OPRD and a OPRI that pass mismatch threshold, which makes things easier +subset(ied, + (opri_pass & oprd_pass)) + +# interesting reads are: + # a- there is a mutation (not reference) + # ! except for PDG 46345 (compound homozygous 1 OPRD / 5 OPRI), for this sample 'reference' may be a somatic mutation + # b- Sanger SV is NA (eg. sCJD cases) or is different than the mutation in the read (not interesting if matches the Sanger genotype) + # c- One of OPRI or OPRD is below mismatch threshold + +# in practice: + # 1- all reads that match what we know from Sanger (so uninteresting here) have a true_nummis number, so can take only true_nummis = NA + # (true_nummis = number of mismatches vs reference, when it matches what is expected) + # by doing so, no need to worry about PDG 46345 (compound homozygous 1 OPRD / 5 OPRI), true_nummis is present for both OPRD1 or OPRI5 reads + # (and is NA if read says reference, as it should) + # 2- ! true_nummis = NA also includes unassigned reads, so need to exclude those + # (! remember to explicitly include othercategory = NA otherwise != excludes NA) + # 3- make use of mismatch threshold, opri_pass or oprd_pass + +iedSom1 <- subset(ied, + is.na(true_nummis) & # 1- + (is.na(othercategory) | othercategory!='unassigned') & # 2- + (opri_pass | oprd_pass | ref_pass)) # 3-, one of opri_pass, oprd_pass, ref_pass is TRUE + + +# Possible somatic mutations: approach 2 ---------------------------------- +# Another approach... + # allows to confirm the above if we reach the same conclusion with two different logics + +# tag the 'expected' reads, i.e. those that do not look like a somatic mutation +ied$expected <- NA # preallocate all as NA + + # all reads whose OPRI matches their sample's SV are 'expected' +ied[which( ied$opri == ied$SV ), 'expected'] <- TRUE + + # all reads whose OPRI matches their sample's SV2 are 'expected' (only applies to PDG 46345) +ied[which( ied$opri == ied$SV2 ), 'expected'] <- TRUE + + # all reads whose OPRD matches their sample's SV are 'expected' +ied[which( ied$oprd == ied$SV ), 'expected'] <- TRUE + + # all reads whose OPRD matches their sample's SV2 are 'expected' (only applies to PDG 46345) +ied[which( ied$oprd == ied$SV2 ), 'expected'] <- TRUE + + # all reads that are reference are 'expected' (! except for PDG 46345, read above) +ied[which( ied$sample != 'pdg46345' & ied$othercategory == 'reference' ), 'expected'] <- TRUE + +# >>> at this stage, expected should tag the same rows as trueread +identical(subset(ied, trueread, read), subset(ied, expected, read)) + + # lots of reads are unassigned to an OPR category + # >> will tag them as expected for simplicity; this will be the difference vs trueread +ied[which( ied$othercategory == 'unassigned' ), 'expected'] <- TRUE + +# great majority of reads should be 'expected' +cat('\t \t \t \t >>> ', sum(ied$expected, na.rm=TRUE), 'out of', nrow(ied), 'considered expected \n') +cat('\t \t \t \t \t i.e.', round((sum(ied$expected, na.rm=TRUE) / nrow(ied))*100, 1), '% \n') + + # tag the rest as 'not expected' (FALSE), i.e. potentially somatic mutation +ied[which(is.na(ied$expected)), 'expected'] <- FALSE + + # check there is no NA left +sum(is.na(ied$expected)) + +# possible somatic = 'not expected', and pass mismatch threshold +iedSom <- subset(ied, + !expected & + (opri_pass | oprd_pass | ref_pass)) # one of opri_pass, oprd_pass, ref_pass is TRUE + + +# >>> does it give the same reads as first logic? +identical(iedSom$read , iedSom1$read) +# yes, same result +# will only keep iedSom +rm(iedSom1) + +# will be useful for later; + # add column 'isSomatic' (TRUE or FALSE) to ied, i.e. this read is a somatic mutation call +ied$isSomatic <- FALSE # preallocate as FALSE (most of them) +ied[match(iedSom$read, ied$read), 'isSomatic'] <- TRUE # for the reads that are in iedSom, replace by TRUE +# put isSomatic in order I want +ied$isSomatic <- factor(ied$isSomatic, levels=c('TRUE', 'FALSE')) + + + + + +# Illustrate mismatch threshold ------------------------------------------- + +# in read length vs number of mismatches; + # plot all 'potentially somatic mutations' reads and colour the ones that pass the mismatch threshold + # the reads that have both OPRI1 and OPRD1 make this annoyingly complicated + # for those, I think will simply plot the minimum mismatch of OPRI/OPRD (read length does not change) + # (to be honest it does not really matter as all of these reads are above the mismatch threshold anyways) + +# all somatic mutations candidates + # (i.e. iedSom from above + all not expected but which does not pass the mismatch threshold) +iedsomall <- subset(ied, + !expected) + +iedsomall$conmis <- NA # number of mismatches vs consensus + +# for reference reads, fill in conmis with reference_nummis +iedsomall[which(!is.na(iedsomall$reference_nummis)) , 'conmis'] <- iedsomall[which(!is.na(iedsomall$reference_nummis)) , 'reference_nummis'] + +# for OPRI reads, fill in conmis with opri_nummis +iedsomall[which(!is.na(iedsomall$opri_nummis)) , 'conmis'] <- iedsomall[which(!is.na(iedsomall$opri_nummis)) , 'opri_nummis'] + +# for OPRD reads, fill in conmis with oprd_nummis +iedsomall[which(!is.na(iedsomall$oprd_nummis)) , 'conmis'] <- iedsomall[which(!is.na(iedsomall$oprd_nummis)) , 'oprd_nummis'] + +# check no more NA +sum(is.na(iedsomall$conmis)) + +# ! now, any reads that has both OPRD & OPRI got the number of mismatches vs OPRD consensus (as OPRD was last) +# for these reads, go back and take the minimum number of mismatches between OPRD and OPRI (the best match) +rows2edit <- which( !is.na(iedsomall$opri) & !is.na(iedsomall$oprd) ) +for (r in rows2edit) { + iedsomall[r,'conmis'] <- min(c(iedsomall[r,'opri_nummis'] , iedsomall[r,'oprd_nummis'])) +} +# >>> we have number of mismatches vs consensus for all candidate somatic mutations + +# mismatch threshold + # mean of % mismatch of all true reads (those that match what we know is there) + sd +thrMis <- mean(ied$true_misbp, na.rm=TRUE) + sd(ied$true_misbp, na.rm=TRUE) # as calculated in needleSam.R + +# control PCR: better to use same threshold as before for consistency +thrMis <- 0.058 + +# more intuitively, the threshold excludes the +1 - (nrow(subset(ied, trueread & true_misbp < thrMis)) / nrow(subset(ied, trueread))) # least accurate reads + + +# on plot, will add markers for reference OPR lengths (eg. reference 123 bp, 1 OPRI = 123 + 24 bp, etc.) +ref <- 9 * 1 * 3 + 8 * 4 * 3 # reference = 1 nonapeptide + 4 octapeptide +# OPR I / D are simply +/- full Rs, so +/- multiples of 8 * 3 = 24 bp +oct <- 8 * 3 + +oprlengths <- c(ref-4*oct, + ref-3*oct, + ref-2*oct, + ref-1*oct, + #ref, + ref+1*oct, + ref+2*oct, + ref+3*oct, + ref+4*oct, + ref+5*oct, + ref+6*oct, + ref+7*oct, + ref+8*oct, + ref+9*oct, + ref+10*oct, + ref+11*oct, + ref+12*oct, + ref+13*oct) + +somMisThr <- ggplot(iedsomall, aes(x=read_length, y=conmis, colour=isSomatic)) + + geom_vline(xintercept=ref, linetype=2, colour='#b0b0b0', size=0.8) + + geom_vline(xintercept=oprlengths, linetype=2, colour='#ebebeb', size=0.8) + + geom_segment(x=0, xend=450, + y=0, yend=450*thrMis, + size=1.0, linetype=2, colour='#595E60') + + geom_point(size=0.8) + + scale_colour_manual(values=somcols) + + coord_cartesian(xlim=c(30,400), ylim=c(0, 100.1)) + # when cropping to 450 bp (see below), no read above 150 mismatches + theme_minimal() + + theme( + legend.position='none', + panel.grid.major.x=element_blank(), + panel.grid.minor.x=element_blank(), + axis.title.x=element_text(size=9, margin = margin(t=0, r=0, b=0, l=0)), + axis.text.x=element_text(size=7, margin = margin(t=0, r=0, b=0, l=0)), + axis.title.y=element_text(size=9, margin = margin(t=0, r=-2, b=0, l=0)), + axis.text.y=element_text(size=7, margin = margin(t=0, r=0, b=0, l=0)), + ) + + xlab('read length') + ylab('mismatches vs template') +somMisThr + +if (exportOrNo) { + ggsave(filename=here('controlPCR', 'somMisThr.pdf'), somMisThr, width=90, height=70, units='mm') +} + +# Note; the few reads above 450 bp are crazy repetitions eg. GCGCGCGCGCGC, I think fair to crop the plot at 450 bp +# (and not somatic calls as they have terrible % mismatch) + + + + +# What are the somatic calls? --------------------------------------------- +# plot calls vs counts +# calls as in eg. OPRD1, OPRI2, etc. + +# somatic OPR calls are separated in 3 columns mostly to allow cases where a read is both OPRD & OPRI + +# but in the calls after mismatch threshold... +subset(iedSom, !is.na(opri) & !is.na(oprd)) # no row is both OPRI/OPRD +# and by definition any read that is reference in $othercategory has to be NA in both OPRI & OPRD +# >>> so we can merge all three columns in one column +iedSom$somOPR <- as.character(poolColumns(iedSom, c('othercategory', 'opri', 'oprd'))) + +# check factor order as I want it +iedSom$somOPR <- factor(iedSom$somOPR, levels=c(sprintf('OPRD%i', 4:1), 'reference', sprintf('OPRI%i', 1:24))) + +# now count number of calls per new OPR +sowp <- iedSom %>% # number of somatic calls by new OPR + group_by(somOPR) %>% + tally(name='nSom') + +# for plot, add a normal OPR bar +sowp2 <- sowp %>% + add_row(somOPR='OPR0', nSom=NA, .after=4) + +sowp2$somOPR <- factor(sowp2$somOPR, levels=c('OPRD4', 'OPRD3', 'OPRD2', 'OPRD1', 'OPR0', 'OPRI1', 'OPRI2', 'OPRI3', 'OPRI4')) + +callsvsnewOPR <- ggplot(sowp2, aes(x=somOPR, y=nSom)) + + geom_col(fill=NA, colour='#4D4D4D', width=0.8) + + theme_minimal() + + theme( + panel.grid.minor.x=element_blank(), + axis.title.x=element_text(size=9, margin = margin(t=2, r=0, b=0, l=0)), + axis.text.x=element_text(angle=90, size=7, margin = margin(t=0, r=0, b=0, l=0)), + axis.title.y=element_text(size=9, margin = margin(t=0, r=2, b=0, l=0)), + axis.text.y=element_text(size=7, margin = margin(t=0, r=0, b=0, l=0)), + ) + + xlab('') + ylab('somatic mutation calls') + + scale_x_discrete(labels=c('4 OPRD', '3 OPRD', '2 OPRD', '1 OPRD', '', '1 OPRI', '2 OPRI', '3 OPRI', '4 OPRI')) +callsvsnewOPR + +if (exportOrNo) { + ggsave(filename=here('controlPCR', 'callsvsnewOPR.pdf'), callsvsnewOPR, width=150, height=100, units='mm') +} + +# as percentage of all reads + +sowp2$somOPRper <- (sowp2$nSom / nrow(ied)) * 100 + + +callsvsnewOPRPer <- ggplot(sowp2, aes(x=somOPR, y=somOPRper)) + + geom_col(fill='#4D4D4D', colour='#4D4D4D', width=0.8, alpha=0.5) + + theme_minimal() + + theme( + panel.grid.minor.x=element_blank(), + axis.title.x=element_text(size=9, margin = margin(t=2, r=0, b=0, l=0)), + axis.text.x=element_text(angle=90, size=7, margin = margin(t=0, r=0, b=0, l=0)), + axis.title.y=element_text(size=9, margin = margin(t=0, r=2, b=0, l=0)), + axis.text.y=element_text(size=7, margin = margin(t=0, r=0, b=0, l=0)), + ) + + xlab('') + ylab('somatic mutation calls (% of reads)') + + scale_x_discrete(labels=c('4 OPRD', '3 OPRD', '2 OPRD', '1 OPRD', '', '1 OPRI', '2 OPRI', '3 OPRI', '4 OPRI')) +callsvsnewOPRPer + +if (exportOrNo) { + ggsave(filename=here('controlPCR', 'callsvsnewOPRPer.pdf'), callsvsnewOPRPer, width=120, height=70, units='mm') +} + +# I do not think I can do in percentages here +# I do not see percentage of 'what' I would do... + + + +# percentage of somatic calls --------------------------------------------- + +100 * (sum(as.logical(ied$isSomatic)) / nrow(ied)) + +# how many 1 OPRD +nrow(iedSom) + +length(which(iedSom$somOPR=='OPRD1')) + + + +# write the somatic calls ------------------------------------------------- + +# export iedSom +write.xlsx(iedSom, file=here('controlPCR', 'conPCR_somaticcalls.xlsx')) \ No newline at end of file diff --git a/controlPCR/conPCR_somaticcalls.xlsx b/controlPCR/conPCR_somaticcalls.xlsx new file mode 100644 index 0000000..8fcc421 Binary files /dev/null and b/controlPCR/conPCR_somaticcalls.xlsx differ