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Cancer variant calling workflow with mutect and changes/additions to the GATK best practices

alons123alons123 HerzliyaMember

Hi all,

I'm working on a cancer variant calling workflow (DNAseq) with MuTect as the variant caller, rather than HaplotypeCaller (due to it's low AF intolerance).
I've gone through the forum and couldn't find a full answer to my inquiry. My question has 2 parts actually:

  1. what changes/additions should I implement in my pipeline/workflow to the GATK Best practices workflow for variant analysis to make it more suitable for cancer variant calling with MuTect, taking into account that I don't have a normal tissue sample, just tumor and an hg19 reference from the bundle:
    https://www.broadinstitute.org/gatk/guide/best-practices?bpm=DNAseq#data-processing-ovw

  2. Is there a difference between the recommended "--known" variants/sites of the GATK's best practices workflow for general variant calling and the one for cancer variant calling with MuTect as the variant caller? Specifically to this article:
    http://gatkforums.broadinstitute.org/discussion/1247/what-should-i-use-as-known-variants-sites-for-running-tool-x

Thank you very much in advance,
Alon

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