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.
Force output of certain regions in GenotypeGVCFs
It is a described problem that when you get your calls in the form of VCF file after GenotypeGVCFs, some of the medically relevant variants may be missing and it's impossible to tell whether they are not reported due to the position being a homozygous reference, or due to low coverage or another sequencing issue.
Is there an option to force certain regions to be output, e.g. from an external BED file etc? Would such an option be a useful addition to this tool?
Thank you in advance.