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Mutect run in HC + PON mode ?

QiangshenlabQiangshenlab Columbia UnviersityMember

The Mutect paper said that "To create this filter, we ran MuTect on a set of normal samples as if they were tumor samples without a matched normal sample in STD mode. From these data, a VCF file is created for the sites that were identified as variant by MuTect in more than one normal sample."

We need run Mutect on each normal sample and then integrate all the VCF by users? Or the panel of normal samples can be input to Mutect and a single run in the HC + PON mode gives a single VCF file? How give a set of normal samples as a input of Mutect?

Best Answer

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MA admin
    Accepted Answer

    You run MuTect on each normal sample individually, then you combine the resulting VCFs and you select the variants that were called in more than one sample. The combination and selection steps can be done with GATK tools.


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