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.
What is purpuse of multiple True Sites in VQSR
I have 3 questions:
1- What is the exact purpose of having both HapMap and Omni True Sites in VQSR, vs just one;
2- If I want to restrict the variant calling to my custom list of positions. Which of the 4 input resources do I reduce to my custom list of positions.
3- If I want to introduce my own custom true sites resource, can I replace HapMap with mine, and assign its variants a prior likelihood of say Q20