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