Question: Kinship Relatedness using plink
0
gravatar for Sharon
2.3 years ago by
Sharon460
Sharon460 wrote:

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.

kinship relatedness • 2.9k views
ADD COMMENTlink modified 2.2 years ago by Biostar ♦♦ 20 • written 2.3 years ago by Sharon460

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

ADD REPLYlink written 2.3 years ago by GabrielMontenegro540
1

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.

ADD REPLYlink written 2.3 years ago by Sharon460

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.

ADD REPLYlink written 2.3 years ago by GabrielMontenegro540
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