Heads up:
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.
We will be out of the office for a Broad Institute event from Dec 10th to Dec 11th 2019. We will be back to monitor the GATK forum on Dec 12th 2019. In the meantime we encourage you to help out other community members with their queries.
Thank you for your patience!

How do MuTect1.1.4 and MuTect2 differ in Tumor only mode (no matched control) variant calling

What is the difference between MuTect1.1.4 and MuTect2 versions in Tumor only mode (no matched control) variant calling method? Is there a preference of using one over the other for this specific application? I would prefer not to use a PON vcf and run tumor only mode to identify variants and use COSMIC/dbSNP to filter out common SNPs. How do I interpret the KEEP vs REJECT calls in this case where there is no matched control to determine somatic variants?


  • davidbendavidben BostonMember, Broadie, Dev ✭✭✭

    @vsundare MuTect1 is obsolete. As of GATK 4, Mutect2 is a complete rewrite. We recommend that you use the best practices workflow using our AF-only gnomAD for the --germline-resource argument. dbSNP will give worse results. The PON is for removing technical artifacts, not germline variants, and therefore should be used when possible. When there is no matched normal a PASS call is Mutect2's best guess and inevitably has some chance of actually being a germline variant.

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