All associations in GWAS Catalog can be downloaded here: https://www.ebi.ac.uk/gwas/docs/file-downloads
However, the Odds Ratios (ORs) from cases/controls studies and the betas from continuous phenotypes are mixed in a single column called "OR_or_beta". Why would they do that? ORs and betas are naturally different; the OR is multiplicative, and the "no effect" OR is 1, while the beta is additive, and the "no effect" beta is 0. The right values to compare would be betas and log(OR).
In contrast, if you visit a particular association on their web, the OR is clearly not mixed with the beta column. Or if you query their RESTful API for one particular association, you get the
betaNum and the
orPerCopyNum as different entries. Since I need to work with the full dataset, I find this annoying.
Any clue on why they mix ORs and betas? And how could I tell them appart in the analysis?