Custom GWAS command line (CLI) tool

You can also launch the Custom GWAS tool from the command line using the finngen-cli tool. 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 and quantitative phenotypes using REGENIE pipeline. You can also run additive, recessive, or dominant analysis.

See instructions on how to:

• Custom GWAS CLI Binary mode

• Custom GWAS CLI Quantitative mode

Tip: Custom GWAS in Binary mode with an additive model can also be launched using the custom GWAS module in the Cohort Operations tool.

Tip: See also General workflows for the most common analyses researchers are conducting with FinnGen data in FinnGen Sandbox.