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Percent of variant reads to make a heterozygous call

I was wondering what is the min percent of variant reads GATK uses by default to make a heterozygous call and how to change this value if need be.

Best Answer


  • Thanks Geraldine.
    Is there a way I can set this threshold?

    Also, where can I get more details about how GATK exactly calls heterozygous allele?


  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie admin

    Have a look at the presentations from recent workshops, a lot of the internal logic is explained there. For the various thresholds that can affect sensitivity, see the HaplotypeCaller tool doc (Guide>Tool Documentation) for a full list of options.

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