How to generate v2d from FinnGen studies


I was wondering whether/how you have processed FinnGen in the v2d_data steps. Did you use the LD reference panel from the FinnGen consortium? I see that finemapping is not performed on FinnGen studies because you take the results generated with SuSIE, and in the colocalisation step no conditioning is performed for FinnGen studies. The v2d steps are the last where I’m wondering what to do if I don’t have access to FinnGen’s LD reference panel.


Hi Roman,

Which steps in the v2d pipelines are you referring to?

As you say, we do not perform fine-mapping for FinnGen studies, the only other step in the v2d is generating the top loci table and study table, neither of which requires FinnGen’s LD panels.

Best wishes,