VS-1310 - VS-1310 changes to echo callset branch

broadinstitute / gatk

Official code repository for GATK versions 4 and up

https://software.broadinstitute.org/gatk

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Closed gbggrant closed 1 month ago

gbggrant commented 1 month ago

Add new parameter to set filtered genotypes to no-calls to ExtractCohort
Modified ExtractCohortEngine to optionally set genotypes that are filtered (FT flag set - at the genotype leve) to no-calls.
Renamed VQSR Classic to 'VQSR'
Renamed VQSR Lite to 'VETS'
Updated VCF and pgen tests for code changes