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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?

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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.

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