# 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.


---

# Agent Instructions: Querying This Documentation

If you need additional information that is not directly available in this page, you can query the documentation dynamically by asking a question.

Perform an HTTP GET request on the current page URL with the `ask` query parameter:

```
GET https://finngen.gitbook.io/documentation/r5/methods/phewas.md?ask=<question>
```

The question should be specific, self-contained, and written in natural language.
The response will contain a direct answer to the question and relevant excerpts and sources from the documentation.

Use this mechanism when the answer is not explicitly present in the current page, you need clarification or additional context, or you want to retrieve related documentation sections.