Sea of genomic wide significant hits in GWAS (Plink2) and Absence when using regenie

Question

[a.papadam]

Hi all,

I recently performed a GWAS on a continuous measurement (the previous GWAS used a relative binary measurement), but when I run PLINK2, it returns thousands of genome-wide hits without forming any clear peaks. In contrast, when I use REGENIE, there are no significant hits.

This could be due to noise, a confounder, or a genuinely polygenic signal with subtle effects.

However, I am unsure how to test each scenario and correct for it if possible. I have tried various covariates in my GWAS, different scaling methods, excluding outliers, etc.

Any insights?

Thanks in advance.