Hello,
as I see from plink documentation to keep only distantly related samples PI_HAT=P(IBD=2)+0.5*P(IBD=1)=0.125 according to this table 1 https://www.sciencedirect.com/science/article/pii/S0002929714004273
but I am unable to find a table which would compare plink --king-cutoff coefficients with PI_HAT explicitly
My guess from what I read is that --king-cutoff 0.0884 would correspond to PI_HAT = 0.125
Can someone please give me some input on this?
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anamaria
The king cutoff is based on a software called KING. You can find more information here: https://people.virginia.edu/~wc9c/KING/manual.html
Based on the document:
an estimated kinship coefficient range >0.354, [0.177, 0.354], [0.0884, 0.177] and [0.0442, 0.0884] corresponds to duplicate/MZ twin, 1st-degree, 2nd-degree, and 3rd-degree relationships respectively
Thanks for sharing that. One thing is unclear to me is it necessary to run: plink --bfile output8 --genome --grm-cutoff 0.1 --make-bed --out output9
after I did run this bellow? plink2 --bfile output7 --king-cutoff 0.0884 plink2 --bfile output7 --remove plink2.king.cutoff.out.id --make-bed --out output8
So you ran plink2 --bfile output7 --king-cutoff 0.0884 plink2 --bfile output7 --remove plink2.king.cutoff.out.id --make-bed --out output8?
where do you get the plink2.king.cutoff.out.id file?
If you have performed king filtering, I don't think you need to do the grm filtering.
Side note: You might want to prune your data before you perform king or grm fitlering
As far as I know, --king-cutoff 0.08 would correspond to PI_HAT = 0.2 because both filter for second-degree relationship. But I tried both in my dataset and diferent individuals were removed. The last removed more than the former. Does anyone know the reason?
If you need to ask, then you should ignore PI_HAT. A major advantage of the KING method is that it is much harder to misuse.
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