search

broadinstitute / gatk-protected

Obsolete/Legacy GATK repository -- go to https://github.com/broadinstitute/gatk instead
BSD 3-Clause "New" or "Revised" License
33 stars 20 forks source link

Is it really necessary to "prepare likelihoods for annotation"? #1112

Closed davidbenjamin closed 7 years ago

davidbenjamin commented 7 years ago

In SomaticGenotypingEngine::callMutations and HaplotypeCallerGenotypingEngine::assignGenotypeLikelihoods there is a line of code after the call is made but before the variant is annotated:

ReadLikelihoods annotationLikelihoods = prepareReadAlleleLikelihoodsForAnnotation(likelihoods...)

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.

droazen commented 7 years ago

Issue moved to broadinstitute/gatk #3022 via ZenHub