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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.
    Solution:
    This error is fixed in master as of March 19th 2019. It will be released in the GATK version 4.1.1.0.
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