how to call somatic of homozygosity?

hi, does gatk support call somatic of homozygosity?

Lets assume, we have a diploid cell (which is not always the case for e.g. tumor cells which can have copy number variations). If variant A (e.g. a SNV) is homozygous, you expect to see 100% of the reads from your exome-seq or wgs (lets assume NGS doesnt produce errors) containing this variant. If this variant is heterozygous (so one chromosome has the variant A and the other has the wildtype B), you expect to see 50% of the reads to contain A and 50% of the reads to contain B.

so is it ok for gatk to do this, thanks a lot

Best Answer

  • manbamanba ✭✭
    Accepted Answer


    is the red bamout means bamout by mutect2? thanks a lot. so the tumor and normal bam refers to the out of just bwa result? if just to compare, should just need reassembly bam and normal, why still need the tumor?

Answers

  • manbamanba Member ✭✭


    you can see the GT is 0/0, this means the same as reference? if so, it must not be a somatic varaint, why still in vcf file?

    thanks a lot

  • manbamanba Member ✭✭
    Accepted Answer


    is the red bamout means bamout by mutect2? thanks a lot. so the tumor and normal bam refers to the out of just bwa result? if just to compare, should just need reassembly bam and normal, why still need the tumor?

  • davidbendavidben BostonMember, Broadie, Dev ✭✭✭

    @manba your red arrow points to the genotype of the normal sample, which is homozygous for the reference allele. The tumor sample is 0/1 -- since we can't assume that tumors are diploid, we don't try to distinguish 0/1 from 1/1.

  • manbamanba Member ✭✭

    @davidben, but you can clearly see that it is a somatic vcf(from the file nam)

  • AdelaideRAdelaideR Unconfirmed, Member, Broadie, Moderator admin

    Hi @manba I think I understand where your confusion might be, a somatic vcf produced by Mutect2 is not interpreted against a reference. Here is some relevant information from this very informative website, which may have answers to your questions

    ```A somatic caller should detect low fraction alleles, can make no explicit ploidy assumption and omits genotyping in the traditional sense. Mutect2 adheres to all of these criteria.

    A number of cancer sample characteristics necessitate such caller features. For one, biopsied tumor samples are commonly contaminated with normal cells, and the normal fraction can be much higher than the tumor fraction of a sample. Second, a tumor can be heterogeneous in its mutations. Third, these mutations not uncommonly include aneuploid events that change the copy number of a cell's genome in patchwork fashion.```

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