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.
MarkIlluminaAdapters missing from GATK pipelines
The best practices GATK exome and genome pipelines seem to not perform adapter clipping/marking with MarkIlluminaAdapters as described here: https://software.broadinstitute.org/gatk/documentation/article?id=6483
This would likely lead to significant issues in subsequent alignments and false positive calls.
Why is MarkIlluminaAdapters not part of the standard GATK pipelines even though the GATK website says it should be?