> 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/working-in-the-sandbox/which-tools-are-available/untitled/custom-gwas-command-line-cli-tool.md).

# Custom GWAS command line (CLI) tool

You can also launch the Custom GWAS tool from the command line using [the finngen-cli tool](/working-in-the-sandbox/running-analyses-in-sandbox/pipelines-tool-instructions/how-to-submit-a-pipeline-from-a-command-line.md). This gives you the **freedom to being able to create files of cases and controls outside Atlas** or **run a phenofile** (the format used by plink and SAIGE).

Via this method your results **will** also **appear in userresults.finngen.fi** once the run has completed.

From the Sandbox v10.2 onward Custom GWAS CLI is available for both [binary](/working-in-the-sandbox/which-tools-are-available/untitled/custom-gwas-command-line-cli-tool/custom-gwas-cli-binary-mode.md) and [quantitative](/working-in-the-sandbox/which-tools-are-available/untitled/custom-gwas-command-line-cli-tool/custom-gwas-cli-quantitative-mode.md) phenotypes using REGENIE pipeline. You can also run additive, recessive, or dominant analysis.

**See** **instructions** on how to:

* [Custom GWAS CLI Binary mode](/working-in-the-sandbox/which-tools-are-available/untitled/custom-gwas-command-line-cli-tool/custom-gwas-cli-binary-mode.md)
* [Custom GWAS CLI Quantitative mode](/working-in-the-sandbox/which-tools-are-available/untitled/custom-gwas-command-line-cli-tool/custom-gwas-cli-quantitative-mode.md)

**Tip:** Custom GWAS in Binary mode with an additive model can also be launched using the [custom GWAS module in the Cohort Operations tool](/working-in-the-sandbox/which-tools-are-available/cohort-operations-tool-co/launch-custom-gwas-with-co.md).

**Tip:** See also [General workflows for the most common analyses](/working-in-the-sandbox/general-workflows-for-the-most-common-analyses.md) researchers are conducting with FinnGen data in FinnGen Sandbox.