Kinship Relatedness using plink

Question

[Sharon]

If the plink PIHAT score between 2 samples is around 0.03, can we say these samples are related even with a 5th degree or 6th degree relatedness? I am trying to prove any relatedness between the samples.

Answer 1

[GabrielMontenegro]

I suggest you to check out this previous post: Ibd (Identity By Descent) And The Chosen Value Of Pi_Hat

[Sharon]

Thank you. What I understand from the replies specially the last reply, is that pihat around 0.03 means 5th degree relatedness but plink filters out from 0.05 to remove any relatedness, that's why I am confused.

[GabrielMontenegro]

Check how PI_HAT is computed in PLINK, specially how IBD is calculated. You will then see that this estimates can be affected for instance by admixture/consanguinity. For example, if your population is highly drifted and/or has experienced various bottlenecks (think of Native Americans say) a PI_HAT value even between unrelated individuals will be much higher than the 0.05 default.