in the INFO column of a Mutect2 VCF only refer to the ALT?

Because a somatic callset is based on a single individual rather than a cohort, annotations in the INFO column of a Mutect2 VCF only refer to the ALT alleles and do not include values for the REF allele. This differs from a germline cohort callset, in which annotations in the INFO field are typically derived from data related to all observed alleles including the reference.

means there is only _TLOD value _in the INFO column of somatic?

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Answers

  • davidbendavidben BostonMember, Broadie, Dev ✭✭✭

    @picard_gatk_mj This depends on the annotation. The vcf header produced by Mutect2 describes the definitions of each INFO and FORMAT annotation.

  • manbamanba Member ✭✭
    edited January 6

    @davidben Thanks a lot
    but I can not understand what does "a somatic callset is based on a single individual rather than a cohort, annotations in the INFO column of a Mutect2 VCF only refer to the ALT alleles and do not include values for the REF allele."
    it means the value in column INFO
    DP=236;ECNT=1;POP_AF=5.000e-08;P_CONTAM=0.00;P_GERMLINE=-4.907e+01;TLOD=32.44
    has nothing to do with ref?
    but I kown POP_AF is sure to has relation with ref, so why here said the annotations in the INFO column do not include values for the REF allele.?

  • davidbendavidben BostonMember, Broadie, Dev ✭✭✭

    @manba I would consult the VCF header emitted by Mutect2 if I were you. It describes all of Mutect2's INFO and FORMAT annotations.

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