Launch Mutect2 + Battenberg + PhyloWGS seeds [HNSC single-region]

[philsteinberg]

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

[philsteinberg]

Running

[philsteinberg]

<prefix>-mutass.json.gz

• mut_assignments, ssms

<prefix>-muts.json.gz

• cnvs

<prefix>-summ.json.gz

• trees, clustering_index, branching_index, populations
• I am guessing this is for drawing the phylogeny/cladogram of the cancer evolution

What information do I extract from which phyloWGS output?

• Num of Subclones
• Num of SNVS
• CCF

[philsteinberg]

Script https://github.com/uclahs-cds/project-CPCGENE-subclonality/blob/ccc7377a82bba591e0868499c83c3cb138e432af/200PT/ssm_cnv_from_json.R