Release notes v0.18.1 and v0.18.2
Fixes
Three notemp fixes: general report input file that were missing as it is only specified in a config and optiype temp directory that removed all output. Also, all temporary files from purecn was removed to avoid checkpoint issues that came up in the v0.18.1.
Release notes v0.18.0
Features
MSI site filtering
Now calculates both filtered and unfiltered MSI scores. The filtered sites are approximately 400 sites chosen to be informative MSI sites reducing noise and enabling us to better differenciate MSI from MSS in Endometrial cancer (ENC)
New fusion caller (JuLI)
Performs similar or better than FuseqWES. Good complement as it finds some new true fusions. Also has a shorter wall-time.
General result report
A general result report for each samples is added where results are collected and links are supplied to various results files in addition to smaple specific QC data.
HLA typing
Added HLA typing of HLA-A, HLA-B, and HLA-C with 4 digit resolution (ie HLA-A*02:01).
Save germline vcf
The germilne vaf could be useful to save in case of for example contamination
Fixes
Correct NA handling of Jumble calls
Jumble does not report BAF values which caused problems in the filtering used in the reports of CNVs. This caused lots of neutral copy variant to pass the filtering. Now missing values return True and the filtering works as expected.
MultiQC DNA
The general table had several lines per sample. This will be fixed in next release.
Reference pipeline: MSI Panel of normal
Corrected the generation of the MSI PoN so that all the steps are run and not only the scan for MSI sites.
Changes in config.yaml
general_report: "config/reports/general_report.yaml"
general_html_report:
final_directory_depth: 4
multiqc_config: "config/reports/multiqc_config_dna.yaml"
juli_annotate:
container: "docker://hydragenetics/juli:0.1.6.2"
juli_call:
container: "docker://hydragenetics/juli:0.1.6.2"
optitype:
container: "docker://fred2/optitype:release-v1.3.1"Changes in config/config.data.hg19.yaml
juli_annotate:
cosmic: "{{PROJECT_REF_DATA}}/ref_data/juli/CosmicFusionExport_V76.tsv"
pfam: "{{PROJECT_REF_DATA}}/ref_data/juli/Pfam-A.full.human"
ref_genes: "{{PROJECT_REF_DATA}}/ref_data/juli/refGene_hg19.txt"
uniprot: "{{PROJECT_REF_DATA}}/ref_data/juli/HGNC_GeneName_UniProtID_160524.txt"
juli_call:
gap_file: "{{PROJECT_REF_DATA}}/ref_data/juli/gap_hg19.txt"
ref_genes: "{{PROJECT_REF_DATA}}/ref_data/juli/refGene_hg19.txt"
msisensor_pro:
=>
msisensor_pro_filter_sites:
PoN: "{{PROJECT_PON_DATA}}/GMS560/PoN/Msisensor_pro_reference_nextseq_36.list_baseline"
msi_sites_bed: "{{PROJECT_PON_DATA}}/GMS560/design/SelectedMSIloci2019Sorted.bed"Hydra modules with releases
- prealignment: v1.0.0 (No change)
- alignment: v0.5.0 (No change)
- snv_indels: v1.1.0 (No change)
- annotation: v1.1.0 (No change)
- filtering: v0.3.0 (No change)
- qc: v0.5.0 (No change)
- biomarker: v0.5.0 (MSI filtering)
- fusions: v0.2.2 (JuLI fusion calling)
- cnv_sv: v0.7.0 (No change)
- reports: v0.6.0 (General results report)
Snakemake min version
7.18.0 (no change)
Hydra genetics min version
3.0.0 (no change)
Hydra genetics common singularity version
3.0.0 (no change)