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 on November 11th and 13th 2019, due to the U.S. holiday(Veteran's day) and due to a team event(Nov 13th). We will return to monitoring the GATK forum on November 12th and 14th respectively. Thank you for your patience.

Mutect2 (v4.1.2.0) INDEL calling

Hi, wondering if there a limitation on indel calling with Mutect2. Although it called some validated INDELS (15bp del, 33bp ins, etc..), I have an 88bp deletion it did not. It was previously picked by HC (v3.2) at ~14% and with v4.1.2 as well at ~9.75%. I understand there will be differences between the two callers, but it is real and not present in PON to be filtered out. Just want to make sure if this is an expected outcome (due to indel length, any filters, etc..)

Re-posting here as seems to be the right place!


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