# Custom GWAS tools

### Trade-offs of different methods

We provide a number of methods that enable you to run GWAS for your custom endpoint(s). This table describes the trade-offs of different methods. All methods use [REGENIE](https://docs.finngen.fi/working-in-the-sandbox/running-analyses-in-sandbox/how-to-run-genome-wide-association-studies-gwas/how-to-run-gwas-using-regenie). There are also instructions to use [SAIGE](https://docs.finngen.fi/working-in-the-sandbox/running-analyses-in-sandbox/how-to-run-genome-wide-association-studies-gwas/how-to-run-gwas-using-saige) available, but since DF7 we have moved to use REGENIE, and SAIGE has not been supported similarly since.

#### The fastest way to get results calculated

The easiest way to get results calculated and out of the sandbox is to use the methods in the first 2 rows - these methods enable the summary statistics to be automatically put into the green bucket and [user.results pheweb browser](https://userresults.finngen.fi).

If you want to browse your results outside of sandbox, the 2 lower methods require that you request to have results downloaded, which can take more time especially off-hours Helsinki time. These methods also require a bit more coding skills. Using these methods, however, you are able to modify some parameters in your job, e.g. covariates.

<figure><img src="https://3072695768-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2F-MhYL0UTLjqsuIdK0SSO%2Fuploads%2Fgit-blob-8510212b93563b652d2dad8d7b1dfa08aa924bcb%2Fimage%20(822).png?alt=media" alt=""><figcaption></figcaption></figure>

In the subsections here we describe the two methods you can use to have your methods visible in userresults.finngen.fi:

* [Custom GWAS GUI tool](https://docs.finngen.fi/working-in-the-sandbox/which-tools-are-available/untitled/custom-gwas-tool)
* [Custom GWAS commandline (CLI) tool](https://docs.finngen.fi/working-in-the-sandbox/which-tools-are-available/untitled/custom-gwas-command-line-cli-tool)

And in the subsections here we describe the two other methods you can use to run GWAS for your custom endpoint:

* [REGENIE pipelines using command line](https://docs.finngen.fi/working-in-the-sandbox/running-analyses-in-sandbox/how-to-run-genome-wide-association-studies-gwas/how-to-run-gwas-using-regenie)
* H[ow to use standard pipelines](https://docs.finngen.fi/running-analyses-in-sandbox/pipelines-tool-instructions/how-to-use-the-pipelines-area#submit-a-standard-job)

However you can learn more about other additional methods under ["How to create a user-defined endpoint"](https://docs.finngen.fi/finngen-data-specifics/endpoints/link-to-how-to-make-a-user-defined-endpoint).

### Upstream analysis

Before entering GWAS consider investigating your phenotype and genotype cohorts. For further instructions see:

* [General workflows for the most common analyses](https://docs.finngen.fi/working-in-the-sandbox/general-workflows-for-the-most-common-analyses) researchers are conducting with FinnGen data in FinnGen Sandbox
* [Trajectory Visualization tool](https://docs.finngen.fi/working-in-the-sandbox/which-tools-are-available/trajectory-visualization-tool-tvt)
* [Cohort Operations tool](https://docs.finngen.fi/working-in-the-sandbox/which-tools-are-available/cohort-operations-tool-co)

### Downstream analysis

After custom GWAS is conducted you may consider further downstream analyses like

* [How to conduct Finemapping](https://docs.finngen.fi/working-in-the-sandbox/running-analyses-in-sandbox/how-to-run-finemapping-pipeline) to assign a probability that each significant variant at a locus is the causal variant. More [background reading about Finemapping](https://docs.finngen.fi/background-reading/finemapping).
* [Multiple Manhattan Plot](https://docs.finngen.fi/working-outside-the-sandbox/multiple-manhattan-plot-mmp) to compare several GWAS summary statistics.