Test-drive the GATK tools and Best Practices pipelines on Terra
Check out this blog post to learn how you can get started with GATK and try out the pipelines in preconfigured workspaces (with a user-friendly interface!) without having to install anything.
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?)?