We used the SAIGE software for running R5 GWAS as we did in previous releases. SAIGE is a mixed model logistic regression R/C++ package. We used code of version 0.36.3.2: https://github.com/weizhouUMICH/SAIGE/tree/finngen_r5_jk We made two modifications to SAIGE 0.36.3.2 codebase (neither modification affects the method):
Null model .rda objects were trimmed to reduce RAM consumption
Het and alt hom counts in cases and controls are included in the output
We included the following covariates in the model: sex, age, 10 PCs, genotyping batch.