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!
Estimating error/mismatch rate by Mutect2
So finally Mutect2 calls variants from multiple tumors, and it's great (at least the SNVs). Now assume we have tumorA and tumorB (from the same individual), and Mutect2 calls a variant in tumorA (high allele fraction), but tumor 2 has only 1-2 reads supporting the variant allele. To be able to decide whether the variant in tumorB exists, we need to estimate the mismatch/error rate, and compare the 1-2 reads seen in tumorB with the expected error rate. We can in general estimate the mismatch rate using Picard CollectAlignmentSummaryMetrics, but the numbers don't seem to reflect the real error rate emitted by Mutect2, likely because Mutect2 applies its own read filters beforehand.
Is there a tool/trick to get the background error rate under Mutect2 filters?