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.
Removing * Alleles
The program I am using for analysis considers * alleles inappropriate for analysis. From my understanding these are spanning deletions, but I am unsure how to properly remove them from my data.
Do you have any recommendations for how I can effectively remove these alleles from my dataset? I've tried every recommendation based on a search in this forum including
-selectTypeToExclude MIXED --selectTypeToExclude SYMBOLIC but to no avail.