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

Thanks
Matt