Somatic SV Workflow

With modifications for CWL integration

Contact Matt Wyczalkowski (m.wyczalkowski@wustl.edu) with questions

Versions

Versions are those indicated in DCC Analysis Summary for CPTAC3 project

Version 2.0

Associated with image mwyczalkowski/somatic_sv:20220217
Manta 1.6.0
Support for tumor/normal and tumor-only modes
Files returned, currently unfiltered:
- Tumor-normal
  - candidateSmallIndels.vcf.gz
  - candidateSV.vcf.gz
  - diploidSV.vcf.gz
  - somaticSV.vcf.gz
- Tumor-only
  - candidateSmallIndels.vcf.gz
  - candidateSV.vcf.gz
  - tumorSV.vcf.gz

Version 1.2

Associated with CWL file "SomaticSV.cwl"
- this is the version used for CPTAC3 processing
Docker image: mwyczalkowski/somatic_sv:20200518
Manta 1.6.0
Filters: Only select the variants from somaticSV.vcf.gz output which pass the following criteria:
- Sample site depth is less than 3x the median chromosome depth near one or both variant breakends
- Somatic score is greater than 30
- For a small variant (<1000 bases) in the normal sample, the fraction of reads with MAPQ0 around either breakend doesn't exceed 0.4
BAM files evidence_0 and evidence_1 generated with Manta argument --generateEvidenceBam

Version 1.1

Manta 1.4.0 with tumor and normal sequence data
Filtering as in v1.2, no BAM evidence files returned

Run Notes

In general, SomaticSV is run using CromwellRunner

Install SomaticSV

git clone --recurse-submodules https://github.com/ding-lab/SomaticSV.git

Development notes

Demo data

For development and testing purposes, we distribute Demo data obtained from Manta distribution in demo/demo_data directory, consisting of small tumor/normal BAM files and a reference. Prior to testing, need to uncompress the reference with,

tar -xvjf Homo_sapiens_assembly19.COST16011_region.fa.tar.bz2

GitHub Contact Matt Wyczalkowski (m.wyczalkowski@wustl.edu) with questions