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.
Questions about the GATK hg38 resource bundle reference
I am using the GATK hg38 resource bundle reference in my workflow and I was curious if there is any documentation or literature on how the contigs were chosen. Specifically, were did all the decoy contigs come from? A second part to my question is how decoy contigs are managed in a variant calling workflow. Are they ignored by Mutect2 or do you have to filter them out?