what pihat cutoffs from plink --genome are 3rd degree relative
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3.6 years ago
curious ▴ 820

I run:

plink --bfile $ld_pruned --genome --out $ld_pruned.ibd

according to this:

  • Identical twins, and duplicates, are 100%identical by descent (Pihat 1.0)
  • First-degree relatives are 50% IBD (Pihat 0.5)
  • Second-degree relatives are 25% IBD (Pihat 0.25)
  • Third-degree relatives are 12.5% equal IBD (Pihat 0.125)

These are the mean proportions, but what are the ranges?

would I assume that Pihat between 18.75 and 9.375 is 3rd degree (halfway between 2nd and third cutoff etc. Is it right? Basically how to use output from that plink command to bin according to relationship degree (Parent offspring, full sibling, 2nd,3rd,etc)

(25 + 12.5) / 2 = 18.75 and ((12.5 / 2) + 12.5) / 2 = 9.375

related ibd plink • 2.3k views
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OP here, while I would assume not perfect, this does seem to be an approach used for at least distant relatives. 1

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