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--badLodCutoff option in VQSR

VQSR documentation says: "You may notice that these recommendations no longer include the --numBadVariants argument. That is because we have removed this argument from the tool, as the VariantRecalibrator now determines the number of variants to use for modeling "bad" variants internally based on the data."

When --badLodCutoff option is specified, does it mean that the "internal" algorithm is not used and the set and number of "bad" variants is simply determined by imposing that cutoff on the raw quality score?


  • NikTuzovNikTuzov Member

    Also, is there more information about the "internal" algorithm?

  • SheilaSheila Broad InstituteMember, Broadie admin


    Yes, that is correct about the --badLodCutoff. For more details on the internal algorithm, the best thing to do is look at the code. We are working on a better algorithm for VQSR, so when that comes out we may consider documenting the internal algorithm in more depth.


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