> 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/r4/methods/phewas.md).

# GWAS

We used the [SAIGE](https://github.com/weizhouUMICH/SAIGE/releases/tag/0.35.8.8) (version 0.35.8.8) software for running the R4 GWAS.

[SAIGE](https://github.com/weizhouUMICH/SAIGE/) is a mixed model logistic regression R/C++ package, able to account for related samples.

We analyzed:

* ​2,444 endpoints
* 176,899 samples
* 16,962,023 variants

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