Downsampling to coverage and the 3.x HaplotypeCaller
I am just wondering about the
--downsample_to_coverage when using HC with
--emitRefConfidence GVCF followed by
What I want to obtain is the same result as when running just HC on BAM files in plain VCF output format with
--downsample_to_coverage option need to be used when calling HC with
--emitRefConfidence GVCF, GenotypeGVCFs or both?