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, 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 or Cohort Operations tool. The Custom GWAS tool sections will walk you through how to run your GWAS using the case and control cohorts that you created using Atlas. The same Custom GWAS can also be launched from the Cohort Operations. The section General workflows for the most common analyses 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). 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, Saige, Plink2, and Gate.

It is recommended you also read sections Pipelines are based on Cromwell and WLD and How to use the Pipelines tool, because you will need these instructions to be able to run your GWAS in Sandbox.