relationship between PI_HAT and --king-cutoff coefficient?
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18 months ago
anamaria ▴ 160

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?

plink pihat ibd • 1.3k views
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18 months ago
Sam ★ 3.8k

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

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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

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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

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