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.
BAM with soft-clipped primer sequences as an input for RevertSam (Tutorial #6483)
Could I use RevertSam on primer-clipped BAM and then MergeBamAlignment using the primer-clipped BAM and uBAM originated from it as input?
I'm analyzing paired-end TruSeq Custom Amplicon panel data, thus the workflow includes soft-clipping primer sequences with BamClipper. How do I implement the soft-clipping step into the data cleaning pipeline offered in the Tutorial #6483?