Question: is it intentional to leave out minimumBaseQuality from HaplotypeCallerBase?

NationalGenomicsInfrastructure / piper

A genomics pipeline build on top of the GATK Queue framework

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Question: is it intentional to leave out minimumBaseQuality from HaplotypeCallerBase? #59

Closed biocyberman closed 9 years ago

biocyberman commented 9 years ago

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 9 years ago

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.