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stand_call_conf and min_base_quality_score options with gvcf
I used to run Haplotype Caller with stand_call_conf and --min_base_quality_score, but have shifted over to using Haplotype Caller to generate a gvcf (I use emitRefConfidence BP_RESOLUTION, as I need ALL sites), then GenotypeGVCFs to create the actual vcf.
The stand_call_conf and --min_base_quality_score, don't work in the GenotypeGVCFs tool - is it not possible to use these options if I do the two step process (HapCaller and GenotypeGVCF?)?