Clumping with r2=0 and 250kb radius in plink

Question

[landscape95]

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!

Answer 1

[chrchang523]

Answered at https://groups.google.com/g/plink2-users/c/h8sK1P0xnOI .

[landscape95]

Thanks so much @chrchang253