Closed philsteinberg closed 1 year ago
logs: /hot/project/method/AlgorithmEvaluation/BNCH-000082-SRCRNDSeed/pipeline-call-src/run-mutect2-battenberg-phylowgs/logs/
/hot/project/method/AlgorithmEvaluation/BNCH-000082-SRCRNDSeed/pipeline-call-src/run-mutect2-battenberg-phylowgs/logs/
output path : /hot/project/method/AlgorithmEvaluation/BNCH-000082-SRCRNDSeed/pipeline-call-src/run-mutect2-battenberg-phylowgs/output/call-SRC-1.0.0-rc.1/ILHNLNEV000001-T001-P01-F/PhyloWGS-2205be1/output/
/hot/project/method/AlgorithmEvaluation/BNCH-000082-SRCRNDSeed/pipeline-call-src/run-mutect2-battenberg-phylowgs/output/call-SRC-1.0.0-rc.1/ILHNLNEV000001-T001-P01-F/PhyloWGS-2205be1/output/
output files (seed 366306, sample ILHNLNEV000001-T001-P01-F):
PhyloWGS-2205be1_366306_ILHNLNEV000001-T001-P01-F_Mutect2-Battenberg-mutass.json.gz
PhyloWGS-2205be1_366306_ILHNLNEV000001-T001-P01-F_Mutect2-Battenberg-muts.json.gz
PhyloWGS-2205be1_366306_ILHNLNEV000001-T001-P01-F_Mutect2-Battenberg-summ.json.gz
Running
<prefix>-mutass.json.gz
<prefix>-muts.json.gz
<prefix>-summ.json.gz
What information do I extract from which phyloWGS output?
Script https://github.com/uclahs-cds/project-CPCGENE-subclonality/blob/ccc7377a82bba591e0868499c83c3cb138e432af/200PT/ssm_cnv_from_json.R
logs:
/hot/project/method/AlgorithmEvaluation/BNCH-000082-SRCRNDSeed/pipeline-call-src/run-mutect2-battenberg-phylowgs/logs/
output path :
/hot/project/method/AlgorithmEvaluation/BNCH-000082-SRCRNDSeed/pipeline-call-src/run-mutect2-battenberg-phylowgs/output/call-SRC-1.0.0-rc.1/ILHNLNEV000001-T001-P01-F/PhyloWGS-2205be1/output/
output files (seed 366306, sample ILHNLNEV000001-T001-P01-F):
PhyloWGS-2205be1_366306_ILHNLNEV000001-T001-P01-F_Mutect2-Battenberg-mutass.json.gz
PhyloWGS-2205be1_366306_ILHNLNEV000001-T001-P01-F_Mutect2-Battenberg-muts.json.gz
PhyloWGS-2205be1_366306_ILHNLNEV000001-T001-P01-F_Mutect2-Battenberg-summ.json.gz