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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