I am performing WGS using the GATK best practice guidelines for the '-ERC GVCF' cohort analysis workflow. If I ran HaplotypeCaller in default mode (i.e. without specifying any particular annotation modules (e.g. -A Coverage, -A FisherStrand, -A QualByDepth) to generate the gvcf files, do I have the option to add these annotation modules when I run Genotype GVCFs? Not sure whether annotation modules requested at the Genotype GVCF step need to also be present in each of the individual gvcf files?
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