Clump by distance only

[Maizy Brasher]

Hi Chris, 

I am working on a project where I ran many GWAS across many traits, and I want to use plink2 to clump them all together and get a total number of loci identified. I want to define loci by distance only, without incorporating LD information (because I have a follow up analysis that will do this in a different way). If I use a command like the one below, setting --clump-r2 to 0, I still need to provide a reference data set, but am I correct in thinking this will essentially just define clumps based on distance so the reference provided does not matter?

plink2 --pfile cX_EUR_final_qc_rmdup_unrel \
    --clump ${files_in_all} \
    --clump-p-field P \
    --clump-kb 1000 \
    --clump-p1 5e-8 \
    --clump-r2 0 \
    --out cX_regenie_xwas-qc_updated_all_models.regenie.filtered.2mbr20.ldclumped

Thank you in advance for your help!

Maizy

[Chris Chang]

Yes, I would expect that command to work as you described.

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