With modifications for CWL integration
Contact Matt Wyczalkowski ([email protected]) with questions
Versions are those indicated in DCC Analysis Summary for CPTAC3 project
- 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
- Tumor-normal
- 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
andevidence_1
generated with Manta argument--generateEvidenceBam
- Manta 1.4.0 with tumor and normal sequence data
- Filtering as in v1.2, no BAM evidence files returned
In general, SomaticSV is run using CromwellRunner
Install SomaticSV
git clone --recurse-submodules https://github.com/ding-lab/SomaticSV.git
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 ([email protected]) with questions