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.

Running Mutect2 on tumor-only mode in Firecloud

Hi, I have exomes for several tumors without any matched normals. I am trying to call mutations using Mutect's tumor-only mode in the featured "Somatic-SNVs-Indels-GATK4" workspace. However, in this workspace, I only see methods for a matched tumor-normal pair or to create a panel of normal. Can you please tell me how can I run Mutect in tumor only mode in Firecloud? Thanks!


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