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Variants for GetPileupSummaries for non-human organisms

Hi there

I am working with mouse matched tumor-normal samples and running somatic calling with Mutect2 (gatk4). I want to run contamination estimation using GetPileupSummaries, but I don't know what I should provide for the common variants (--variant) option.

Would it be at all helpful to use variants called with haplotypecaller from normal samples? I only have ~5 normals, so the numbers are very small...

Issue · Github
by Sheila

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Best Answers


  • SheilaSheila Broad InstituteMember, Broadie admin


    Hmm. I don't know if you do anything in your case, but I need to check with the team and get back to you.


  • vsvintivsvinti Member ✭✭

    Thanks @Sheila, looking forward to hearing back from you ..

  • vsvintivsvinti Member ✭✭

    Thanks everyone for the helpful answers. I'll just leave it out for now!

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