How to Clump In Plink?

Question

[Thorerges]

I am trying to find the set of independent SNPs for an all european GWAS - i.e clumping.

I haven't used PLINK before, but it seems the obvious tool to do this. The command primarily being:

plink --file mydata --clump mytest1.assoc

Just to be clear what file is what, is mydata here - the LD reference panel? Whereas mytest1.assoc is the actual summary stats file?

Answer 1

[Yong]

The following is an example of script for clumping, you could adjust the parameters as needed:

plink --bfile  1000G_EUR \                                ### The LD reference panel
         --clump MetaGWAS.assoc \                         ### Your summary stats file
         --clump-p1 5e-6 \                                ### Significance threshold for index SNPs
         --clump-p2 0.05 \                                ### Secondary significance threshold for clumped SNPs
         --clump-r2 0.05 \                                ### LD threshold for clumping
        --out MetaGWAS_CAD_clumped_r0.05