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uclahs-cds / project-method-AlgorithmEvaluation-BNCH-000082-SRCRNDSeed

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PhyloWGS seed + sample combinations that failed due to 100% multiprimary trees #95

Closed philsteinberg closed 1 year ago

philsteinberg commented 1 year ago 
    `  Exception: 100% of trees are multiprimary (2500 of 2500), so not enough to report good posterior.`

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

philsteinberg commented 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