analysis germline CNV (exon-level and gene-level) from capture data

Usage

perl GeExCNV.pl -bam /path/to/test.bam -cfg /path/to/cfg.txt -rpt /path/to/rpt.gene.list -outdir /path/to/outdir

Note: if /path/to/outdir does not exist, GeExCNV.pl will automatically make it.

Before running this pipeline, you need to construct some files.

1. reference files
2. annot files

how to construct these files

1. reference files

perl /path/GeExCNV/bin/cal_depth.pl -bam /path/to/test.bam -bed /path/to/bed -samtools /path/to/samtools -outdir /path/to/outdir

this will creat a file *.normalized_depth.txt

you need to copy all these ref files into control dir, see ctr_dir in cfg.txt file.

2. annot files

bedtools intersect -a /path/to/test.bed -b /path/GeExCNV/public_db/geneNM.xls -wo >xxx.annot.xls

less xxx.annot.xls | grep "BRCA1" | grep "NM_007294" >xxx.annot.rpt.xls

less xxx.annot.xls | grep "BRCA2" | grep "NM_000059" >>xxx.annot.rpt.xls

Note:

1. if you want to report other genes' exon-level CNV, you should add it just like above BRCA1/2 lines less xxx.annot.xls | grep ...
2. you need to give the porper transcript for your gene

Testing

see /path/GeExCNV/test/run.sh for detail usage.

Result Dir

you can see /path/GeExCNV/test/test_result/ for detail info.

-rw-rw-r-- 1 fulongfei fulongfei 225275 9月   3 10:32 BB20022818_CL01167.annot.xls
-rw-rw-r-- 1 fulongfei fulongfei  15855 9月   3 10:33 BB20022818_CL01167.CNV.pdf
-rw-rw-r-- 1 fulongfei fulongfei 362679 9月   3 10:33 BB20022818_CL01167.CNV.png
-rw-rw-r-- 1 fulongfei fulongfei     63 9月   3 10:33 BB20022818_CL01167.exon.CNV.xls
-rw-rw-r-- 1 fulongfei fulongfei    449 9月   3 10:33 BB20022818_CL01167.flagstat.txt
-rw-rw-r-- 1 fulongfei fulongfei     58 9月   3 10:33 BB20022818_CL01167.gene.CNV.xls
-rw-rw-r-- 1 fulongfei fulongfei  81200 9月   3 10:32 BB20022818_CL01167.normalized_depth.txt
-rw-rw-r-- 1 fulongfei fulongfei    170 9月   3 10:33 BB20022818_CL01167.QC.xls
-rw-rw-r-- 1 fulongfei fulongfei 136889 9月   3 10:32 BB20022818_CL01167.ratio.xls
-rw-rw-r-- 1 fulongfei fulongfei    144 9月   3 10:33 BB20022818_CL01167.rpt.cnv.xls
-rw-rw-r-- 1 fulongfei fulongfei    549 9月   3 10:05 cfg.log
-rw-rw-r-- 1 fulongfei fulongfei   2796 9月   3 10:05 cnv_BB20022818_CL01167.sh
-rw-rw-r-- 1 fulongfei fulongfei  61534 9月   3 10:32 depth.txt
-rw-rw-r-- 1 fulongfei fulongfei 169742 9月   3 10:32 ref_matrix.xls
-rw-rw-r-- 1 fulongfei fulongfei   2583 9月   3 10:32 selected_ref.txt

Result explain:

cfg.log: detail info in cfg.txt

cnv_BB20022818_CL01167.sh: the shell made after you run main script perl GeExCNV.pl ..., you can sh *.sh or qsub *.sh

depth.txt: depth info

BB20022818_CL01167.normalized_depth.txt: normalized depth info

selected_ref.txt: selected ref samples

ref_matrix.xls: each line is a region in your bed file

BB20022818_CL01167.ratio.xls: copy number ratio info

BB20022818_CL01167.annot.xls: add some annot info

BB20022818_CL01167.flagstat.txt: samtools flagstat info

BB20022818_CL01167.QC.xls: QC info

BB20022818_CL01167.exon.CNV.xls: exon-level cnv result

BB20022818_CL01167.gene.CNV.xls: gene-level cnv result

BB20022818_CL01167.rpt.cnv.xls: final exon-level cnv result

BB20022818_CL01167.CNV.pdf: pdf fig

BB20022818_CL01167.CNV.png: png fig, same as pdf fig

Questions

• how many wbc samples should be used as reference?

at least 30-50 wbc samples are preferred.

Softwares dependencies

• perl
• samtools
• bedtools
• R