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  • allele frequency threshold GATK

    Dear NGS Users,
    I have a question about GATK unified genotyper.
    How can I set allele frequency threshold in the variant calling?

    For example,
    Reference sequence T
    GATK calls T>C variant with 80count per T e 7count for C.
    I would like to set a minor allele frequency of 25% for the calls.
    Anyone has any idea?
    Thanks a lot

  • #2
    Do you mean remove variants with frequency greater than 25%? I think you can use the SelectVariants tool and include the expression:

    --select_expressions "AF>0.25"

    Comment


    • #3
      Yes, thank you very much!!
      Any advice for the threshold for BaseQRankSum and MQRankSum scores to filter out bad variant called?

      Thank u again
      ME

      Comment


      • #4
        Sorry, I am not sure. I am working with a non-model organism, so I do not have a set of validated SNPs to train the program. But if you have such a set that you can download, you can use variant quality score recalibration (http://www.broadinstitute.org/gsa/wi..._recalibration) to calculate VQSLOD, then choose a threshold for that value.

        Not sure if you saw this, but I basically followed the directions given here:

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