GCTA-COJO slct conceptual question

Question

[brighteyes1017]

Hello,

I was wondering if anyone could clarify something about GCTA- COJO, specifically COJO-slct I think.

I understand that it is a tool that performs stepwise model selection to select independently associated SNPs. Does it first identify index SNPs upon which to condition? Or do I need to identify index SNPs first through LD clumping?

Background is that I've done a meta analysis on a few cohorts and want to identify independent SNPs.

Thank you!