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.
Using Tophat "accepted_hits.bam" file for RNAseq variant calling with GATK
Hi, I have some doubts about variant calling in RNAseq data.
So far, I have aligned the reads to a reference (human hg38) genome using Tophat. However, I have seen in your workflow for variant discovery in RNAseq that you recommend to use STAR. Is this really necessary? Could I use the "accepted_hits.bam" file from Tophat instead of the STAR output? would the rest of the workflow remain the same?
Thanks for your help