relationship between PI_HAT and --king-cutoff coefficient?
as I see from plink documentation to keep only distantly related samples
according to this table 1
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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The king cutoff is based on a software called KING. You can find more information here:
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
2.9 years ago by
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?
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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
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