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plink2 --assoc followed by LD clumping #107

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Shicheng-Guo opened this issue Sep 25, 2021 · 1 comment
Open

plink2 --assoc followed by LD clumping #107

Shicheng-Guo opened this issue Sep 25, 2021 · 1 comment

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@Shicheng-Guo
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Dear Gao:
I am wondering what's the best practice to combine plink2 --assoc with --clump to only report association results of independent lead SNPs?
Thanks.
Shicheng
@gaow
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gaow commented Sep 27, 2021

@Shicheng-Guo my preferred practice is to perform GWAS for all SNPs then run clumping as a separate procedure. That way, I have all results somewhere in case I need it down the road, eg for fine-mapping applications as a next step, having only the independent lead SNPs is not sufficient.

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@gaow @Shicheng-Guo