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Allelic Coverage Pulldown at genomic loci

ncamardancamarda DFCIMember, Broadie

Is there a GATK tool that can pull down the allelic coverage at a site in the genome for all alleles? The output format I'm imaging is (A,C,T,G) counts for each genomic loci I specify. Can someone please advise?
Thank you so much.

Best Answer

Answers

  • ncamardancamarda DFCIMember, Broadie

    Hi Sheila, I've been using the DepthOfCoverage tool from GATK 3.8.0 and this has been satisfactory for my purposes. Because none of the somatic variant calling tools in the GATK perform joint calling on tumor samples, I've been trying to implement a force-caller, and for this, I need to be able to identify whether - across samples - a given base has been covered. I've found that it's not necessarily true that the alleles that M2 emits for a given site encompass all of the bases that have coverage at that location.

    Do you think the GATK will ever implement such joint calling for MuTect2?

  • SheilaSheila admin Broad InstituteMember, Broadie, Moderator admin

    @ncamarda
    Hi,

    I remember asking the team about this, and the response was no. I cannot find the exact thread that discusses this, but perhaps this thread will help.

    -Sheila

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