VQSR in variants on X chromosome
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My questions is about VQSR in variants on chr X. How do I know the VQSR values of variants in chr X are computed with consideration of sex and PARs? In other words, I wonder if VQSR of variants on chr x should be computed within females. Likewise, should we remove the PARs and recompute VQSR for the variants on chr X?
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Hi Jaeyoon Chung, thanks for posting this question, I would recommend checking out the algorithms page within our documentation to get more info about VQSR.
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Jaeyoon what did you end up doing? I had the same question.
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