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 not detecting variant visible in tumor and matched cell line bam
I am unable to detect a particular variant when running Mutect2 on a tumor and tumor-derived cell line exome data. I ran each with the corresponding matched normal. The image below displays, from top to bottom: 1) input bam of cell line 2) bamout of cell line 3) input bam of tumor 4) bamout of tumor.
I have had some success in cases where mutect2 didn't detect a visible variant by running again with a focal interval file. No such luck here. Do you have guidance on troubleshooting?