We’re moving the GATK website, docs and forum to a new platform. Read the full story and breakdown of key changes on this blog.
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.
MuTect2 and Alternate Allele Calls
We have a few calls in our dataset that are slightly confusing. We are getting a triallelic flag, which is expected, but only getting one alternate allele outputted to the VCF. The alternate allele that is being called is at <1% VAF, whereas the other alternate is in the 35-40% range, and is a common somatic variant. Any ideas on how to force the calling of these more frequent alternate alleles?