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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.

FilterMutectCalls stats

FilterMutectCalls reports the learned parameters of somatic clustering in a new .filtering_stats.tsv output. This file also contains information on the probability threshold chosen to optimize the F score and the number of false positives and false negatives from each filter to be expected from this choice.

so how should I understand this filter stats(version 4.1.1.0)

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