I am analyzing a family-based whole-genome sequence (WGS) dataset. My identity-by-descent(IBD) analysis shows they share about 50% of their DNA. I think my pedigree structure may have gotten mixed up though and I want to see if one individual is the mother or the sister of a male individual. Is there anyway to do this either with Plink or KING?
With at least three samples, you can determine this by looking at the IBS0 output column (from either plink2 --make-king-table or KING): if the relationship in question has a very low IBS0 value compared to the other pairs, that's parent-child. You can try to do the same thing with only two samples, but with no other IBS0 values to compare against it's easier to misjudge.