If you happen to see a question you know the answer to, please do chime in and help your fellow community members. We encourage our fourm members to be more involved, jump in and help out your fellow researchers with their questions. GATK forum is a community forum and helping each other with using GATK tools and research is the cornerstone of our success as a genomics research community.We appreciate your help!
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.
We will be out of the office on November 11th and 13th 2019, due to the U.S. holiday(Veteran's day) and due to a team event(Nov 13th). We will return to monitoring the GATK forum on November 12th and 14th respectively. Thank you for your patience.
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.