MuTect support for indel calling?

JayendraJayendra KalyaniMember

I have been using MuTect and missing out on important indels in the data.
Is there any option of calling indels in MuTect?
or should I be using GATK unified genotyper for indel calling?

Answers

  • JiantaoShiJiantaoShi BostonMember

    MuTect is designed to find single point mutation. So you may want to try Indelocator, but currently it is not supported. They have a successor method coming.

    Jiantao

    @Jayendra said:
    I have been using MuTect and missing out on important indels in the data.
    Is there any option of calling indels in MuTect?
    or should I be using GATK unified genotyper for indel calling?

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