Entering edit mode
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
OP here, while I would assume not perfect, this does seem to be an approach used for at least distant relatives. 1