In SomaticGenotypingEngine::callMutations and HaplotypeCallerGenotypingEngine::assignGenotypeLikelihoods there is a line of code after the call is made but before the variant is annotated:
Is this really necessary? It seems quite defensible to annotate using the same likelihoods from which the variant call is derived. As far as Mutect is concerned, the standard will be whether our validations are better or at least no worse without it.
In
SomaticGenotypingEngine::callMutations
andHaplotypeCallerGenotypingEngine::assignGenotypeLikelihoods
there is a line of code after the call is made but before the variant is annotated:Is this really necessary? It seems quite defensible to annotate using the same likelihoods from which the variant call is derived. As far as Mutect is concerned, the standard will be whether our validations are better or at least no worse without it.