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.

Known Issues with Mutect2 GATK4.1

bhanuGandhambhanuGandham Cambridge MAMember, Administrator, Broadie, Moderator admin
edited March 20 in Solutions to Problems
  • Error:
    java.lang.IllegalArgumentException: log10p: Log10-probability must be 0 or less when running FilterMutectCalls(GATK4.1) to Filter VCF results called by Mutect2.
    This error is fixed in master as of March 19th 2019. It will be released in the GATK version
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