Pedigree checks

KathKath Posts: 43Member

Hi,

Are there any GATK tools that can be used to check that samples in a pedigree are not mislabelled by looking for Mendelian inconsistencies in the exome sequencing data?

Thanks

Kath

Answers

  • Geraldine_VdAuweraGeraldine_VdAuwera Posts: 8,027Administrator, GATK Dev admin

    Hi Kath,

    You can use the phasing tools to detect mendelian violations, however this is meant to catch de novo mutations, not mislabeled data.

    Geraldine Van der Auwera, PhD

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