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InbreedingCoeff calculation with trio, pairs, singletons etc
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?
- GenotypeGVCFs entire cohort
- Use SelectVariants to extract genetically unrelated individuals (>10)
- Re-apply InbreedingCoeff annotation on the new VCF using VariantAnnotator
- Annotate original (full) VCF with InbreedingCoeff annotations calculated in step 3 (VariantAnnotator)
- Resume BPGs with VQSR