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Joint calling in trios using UnifiedGenotyper

KathKath Member Posts: 43


I have exome data for a few sets of parent-offspring trios, in which offspring have phenotypically related but probably genetically different diseases. Their parents are unaffected so I am particularly interested in identifying de novo mutations. My plan was to analyse each individual separately up to the variant calling phase and then to input three (mother, father, child) analysis-ready BAMs into the UnifiedGenotyper along with a ped file. My questions are:

1) Can you tell me whether the UnifiedGenotyper uses pedigree information in the ped file to call genotypes more accurately? In other words, is this better than calling variants jointly without supplying the ped file? If not, does GATK recommend any external tools for doing this step?

2) It is better to call variants jointly using all the trios (even though they are not related and probably don't share the same disease-causing mutations)?

Best wishes,



  • Geraldine_VdAuweraGeraldine_VdAuwera Administrator, Dev Posts: 11,130 admin

    Hi Kath,

    1. No, the UG does not make use of pedigree information. Several GATK tools use PED info downstream of calling, for example for phasing, evaluating mendelian violations and so on.

    2. You should definitely call members of each trio together. As for calling all trios together, it is unlikely to yield any added benefit if the genetics of the diseases are unrelated, but it can't hurt to do it if you have the computing power.

    Geraldine Van der Auwera, PhD

  • KathKath Member Posts: 43

    Thanks for your help,

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