GATK Unified Genotyper multiple-sample

liujieliujie GermanyMember

When I use Unified Genotyper with multiple-sample, the samples should be of the same kind ? Can I put the cancer samples and normal samples together ?

Answers

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie admin

    Hi @liujie,

    You should not be calling variants on cancer samples with the GATK callers, because they are not designed to deal with cancer-specific error models. You should use MuTect instead. If you have paired tumor and normal samples, MuTect will be able to process them together intelligently.

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