-
Notifications
You must be signed in to change notification settings - Fork 43
New issue
Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.
By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.
Already on GitHub? Sign in to your account
plink2 --assoc followed by LD clumping #107
Comments
@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. |
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
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
The text was updated successfully, but these errors were encountered: