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InbreedingCoeff calculation with trio, pairs, singletons etc

Hi Team

I plan to filter FPs on a cohort of 200 exomes using VQSR. I understand filtering on InbreedingCoeff is not suitable when family relations are present unless specified in a PED file. My issue is the cohort contains sibling pairs and other unsupported family structures.

Do you think this workaround will work OK?

  1. GenotypeGVCFs entire cohort
  2. Use SelectVariants to extract genetically unrelated individuals (>10)
  3. Re-apply InbreedingCoeff annotation on the new VCF using VariantAnnotator
  4. Annotate original (full) VCF with InbreedingCoeff annotations calculated in step 3 (VariantAnnotator)
  5. Resume BPGs with VQSR



  • SheilaSheila Broad InstituteMember, Broadie admin

    Hi Matt,

    Your workflow looks fine, but keep in mind we have not tested this out so we cannot confirm this will work.

    You may try (in step 2) to get as many unrelated samples as possible (you mentioned >10, but the more the merrier in this case :smile: ). You can also try out ExcessHet which is better in larger cohorts.


    P.S. Let us know how it goes!

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