Question: is it intentional to leave out minimumBaseQuality from HaplotypeCallerBase?
biocyberman opened this issue · 1 comments
biocyberman commented
I was checking /src/main/scala/molmed/utils/VariantCallingUtils.scala and found that the parameter minimumBaseQuality is not used for HaplotypeCallerBase where it is used in UnifiedGenotyperSnpCall. Is this intentional, and what is the rationale for doing that?
johandahlberg commented
Well this has to be a miss on my part. Well spotted! Changed this from a question to a bug so that it gets on the todo list.