Thanks so much @chrchang253
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Hi, I am doing clumping with the follow command:
plink \
--bfile ${myfilename} \
--keep all_hg38_EUR.ids \
--clump ${trait}_tmp2.txt \
--clump-snp-field SNP \
--clump-field P \
--allow-extra-chr \
--memory 30000 \
--clump-p1 5e-8 \
--clump-r2 0 \
--clump-kb 250 \
--out ${trait}
I set radius = 250 and r2=0,. To what I understand, pilnk will harvest all SNPs around the index SNPs at radius 250 but from the result, I have 2 SNPs with distance < 250kb, i.e. 14:30847595:C:T and 14:30864928:T:A (17kb)
My plink version: PLINK v1.90b7.1 64-bit (18 Oct 2023)
Can I confirm what I understand is correct and how could this result happen?
Thank you very much!
Answered at https://groups.google.com/g/plink2-users/c/h8sK1P0xnOI .
Thanks so much @chrchang253
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