> For the complete documentation index, see [llms.txt](https://docs.finngen.fi/llms.txt). Markdown versions of documentation pages are available by appending `.md` to page URLs; this page is available as [Markdown](https://docs.finngen.fi/where-to-begin.../how-do-i-run-a-gwas-of-a-phenotype-i-create-myself.md).

# How do I run a GWAS of a phenotype I created myself?

### Custom GWAS tool

When you have successfully created your own endpoint by following the instructions in [How to make a custom endpoint](/where-to-begin.../how-do-i-make-a-custom-endpoint.md), you might then want to run a GWAS on it.

The easiest way to run a GWAS, without any programming experience, is to use the [Custom GWAS tool](/working-in-the-sandbox/which-tools-are-available/untitled.md) or [Cohort Operations](/working-in-the-sandbox/which-tools-are-available/cohort-operations-tool-co.md) tool. The [Custom GWAS tool](/working-in-the-sandbox/which-tools-are-available/untitled.md) sections will walk you through how to run your GWAS using the [case and control cohorts](/working-in-the-sandbox/which-tools-are-available/atlas/detailed-guide/how-to-define-a-cohort-in-atlas.md) that you created using [Atlas](/working-in-the-sandbox/which-tools-are-available/atlas.md). The same Custom GWAS can also be launched from the [Cohort Operations](/working-in-the-sandbox/which-tools-are-available/cohort-operations-tool-co.md). The section [General workflows for the most common analyses](/working-in-the-sandbox/general-workflows-for-the-most-common-analyses.md) describe the most common workflows researchers are conducting in the Sandbox with the FinnGen data. These methods need no programming skills.

### Command Line

If you are more skilled at programming, or if you did not create your endpoint using Atlas, you can run GWAS using the command line. Take a look at the section [How to run genome-wide association studies (GWAS)](/working-in-the-sandbox/running-analyses-in-sandbox/how-to-run-genome-wide-association-studies-gwas.md). The section starts with advice on how to choose a program to use for analysis based on your needs, and continues to sections instructing how to run GWAS in [Regenie](/working-in-the-sandbox/running-analyses-in-sandbox/how-to-run-genome-wide-association-studies-gwas/how-to-run-gwas-using-regenie.md), [Saige](/working-in-the-sandbox/running-analyses-in-sandbox/how-to-run-genome-wide-association-studies-gwas/how-to-run-gwas-using-saige.md), [Plink2](/working-in-the-sandbox/running-analyses-in-sandbox/how-to-run-genome-wide-association-studies-gwas/how-to-run-gwas-using-plink2-for-unrelated-individuals-only.md), and [Gate](/working-in-the-sandbox/running-analyses-in-sandbox/how-to-run-genome-wide-association-studies-gwas/how-to-run-gwas-using-gate-survival-models.md).

It is recommended you also read sections [Pipelines are based on Cromwell and WLD](/working-in-the-sandbox/running-analyses-in-sandbox/pipelines-tool-instructions/pipelines-is-based-on-cromwell-and-wdl.md) and [How to use the Pipelines tool](/working-in-the-sandbox/running-analyses-in-sandbox/pipelines-tool-instructions/how-to-use-the-pipelines-area.md), because you will need these instructions to be able to run your GWAS in [Sandbox](/working-in-the-sandbox.md).