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.
GATK best pratices for RNA-seq somatic mutation finding
I have followed GATK best practices for finding Somatic mutations from cancer versus normal sample from RNA-seq data using Mutect2 as the final caller and rest all quality control steps as per GATK best practices for RNA-seq. But the resulting filtered sets are false positives as we tried to validate them in the wet lab. So we are now planning to call somatic variants using haplotype caller as per guidelines in GTAK practices, please someone who has experience with this caller comment on this.How is it with Haplotype caller, I would like to know the Sensitivity and specificity rate, also the parameters used in the caller to get true positive variants.