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Pedigree checks

KathKath Posts: 43Member


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?




  • Geraldine_VdAuweraGeraldine_VdAuwera Posts: 10,557Administrator, 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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