> For the complete documentation index, see [llms.txt](https://finngen.gitbook.io/documentation/llms.txt). Markdown versions of documentation pages are available by appending `.md` to page URLs; this page is available as [Markdown](https://finngen.gitbook.io/documentation/r5/methods/phewas.md).

# GWAS

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  <br>](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 analyzed:

* ​2,803 endpoints
* 218,792 samples
* 16,962,023 variants

We included the following covariates in the model: sex, age, 10 PCs, genotyping batch.