Closed philsteinberg closed 1 year ago
Mutect2-Battenberg-PhyloWGS-sr /hot/project/method/AlgorithmEvaluation/BNCH-000082-SRCRNDSeed/pipeline-call-src/run-mutect2-battenberg-phylowgs/logs/
Failed runs:
Seed 13142
Seed 253505
ILHNLNEV000004-T001-P01-F
Seed 366306
Seed 659767
Seed 97782
Seed 51404
Seed 423647
Seed 50135
Seed 628019
Seed 838004
You are right the crux of the issue is here, basically PhyloWGS is finding solutions of multiple primaries (independent tumours arising in the same organ that are not from the same ancestor clone). When we initially tested PhyloWGS, we found this solution highly unlikely at the rate that PhyloWGS was calling it, and they decided to ban it. Essentially this just means that PhyloWGS failed for this sample + seed.
We can just make a note that it failed, or if you want to be thorough, you can try digging for the appropriate flag in their code and adding it, just so that we save the multiple primary solution (they call it polyclonal, when we say polyconal we mean something else).
Originally posted by @lydiayliu in https://github.com/uclahs-cds/project-method-AlgorithmEvaluation-BNCH-000082-SRCRNDSeed/issues/94#issuecomment-1357840702