> 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/r2/methods/phewas.md).

# GWAS

We used the [SAIGE](https://github.com/weizhouUMICH/SAIGE/) software for running the R2 GWAS.&#x20;

[SAIGE](https://github.com/weizhouUMICH/SAIGE/) is a mixed model logistic regression R/C++ package, able to account for related samples.&#x20;

We analyzed:

* ​1,122 endpoints
* 96,499 samples
* 17,054,975 variants

We included the following covariates in the model: sex, age, 10 PCs, genotyping batch.&#x20;