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.
Why do BAM files have to be correctly formatted before Picard RevertSam?
After completing tutorial #6483 on mapping and cleaning up short read data efficiently, I tried this with our lab's own BAM files. However, when completing the first step (generate a uBAM from an aligned BAM), I found that I had to use Picard CleanSam and AddOrReplaceReadGroups in order for RevertSam to properly work. I was under the impression that the workflow in the tutorial would be used, at least partially, for BAM files that are not properly formatted for GATK analysis. Is there an intuition as to why I had to format the original BAM file before beginning this process? It seems like those steps could be done after realigning with bwa mem.