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calling germline and somatic mutation simultaneously using GATK4 Mutect2

xiang_zuoxiang_zuo shanghaiMember

Hi, can I call germline and somatic mutation simultaneously using GATK4 Mutect2? Is it possible?

Answers

  • SheilaSheila Broad InstituteMember, Broadie, Moderator admin
    edited May 2018

    @xiang_zuo
    Hi,

    No, we recommend using HaplotypeCaller for calling germline variants and Mutect2 for somatic mutations.

    Mutect2 does have an option to emit "germline variants", but those are not all germline variants; they are just the variants that are present in the matched normal sample and in the tumor sample.

    -Sheila

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