Custom GWAS GUI tool

Step 1:

First make your two cohorts, cases and controls, using Atlas (see How to define a cohort in Atlas). Then, open the Custom GWAS tool:

Step 2:

On the Custom GWAS main page, select ANALYSIS > Next. (If you'd like, you can also view recent GWAS runs by clicking the page RECENTS).

Step 3:

First select the data release you want to use. NB! Cohorts in Atlas must be generated on the same data release as you will run them in Custom GWAS or you will get an error. (In Atlas it is simple to update to a later data release - you can take a cohort and on the "Generate" tab just rerun it for the datafreeze you want to use for GWAS). Usually you will want to use the latest datafreeze to have as many individuals as possible in your GWAS.

Select your case and control cohorts that you created in step 1. For this mock example, we will be using a custom definition of the excessive earwax phenotype. Click next.

Step 4:

The Custom GWAS tool runs a file check and prints summary results like the counts and age distributions of cases and controls. Click Next. The minimum count of cases or control cohort is 20. Custom GWAS runs with cases or control cohort counts of less than 20 will fail.

Step 5:

Fill in a description of your analysis, and specify how your cases and controls were selected. Be as specific as possible - the results of your custom GWAS will be accessible to other FinnGen authorised users, so it's useful if you can specify the exact ICD, NOMESCO or KELA codes you used in building your cohort. Click Next.

Step 6:

Check the box next to “send me a notification when analysis is ready” and put your e-mail address into the "Notification address" field. This will ensure you are notified as soon as the run is done. Press Submit.

Step 7:

You can also follow the progress of your custom GWAS run from the RECENTS menu. The passed column will show for analyses that have succeeded, for those that have failed, and if the analysis is currently running. Custom GWAS jobs will also appear on the front page of the pipelines tool. If your pipeline job fails check the error report from the pipeline job folder.

Step 8:

View your GWAS results

In a web browser outside the Sandbox, for recent user results since the release of DF11 (May 2023) go to https://userresults.finngen.fi. For older user results go to https://userresults-old.finngen.fi/.

First, sign in with your FinnGen user account:

Search for your analysis using the title you assigned your custom GWAS (for example, as shown below, ”Excessive Earwax, wider code usage”). On this page, you can find the phenotype summary and description as well as the genetic results and tables.

After completion or failure of the GWAS, it can be found from multiple sources. A successful GWAS can be found from PheWeb a day after it was completed.

Summary files and plots for custom GWAS runs are also available in the green library at https://console.cloud.google.com/storage/browser/finngen-production-library-green/finngen_R<no>/sandbox_custom_gwas/<phenotype_name>. Where <no> is the data freeze number and <phenotype_name> is the name user give for the phenotype in Step 5. From Sandbox v 11.0 onwards the metadata file will be exported to the green library with the summary data. The final number of cases and controls in the GWAS run can be checked from the metadata file.

All custom GWAS results tables are saved in the Cromwell jobs directory in Sandbox /finngen/pipeline/cromwell/workflows/[workflow_name]/[workflow_ID]. For example, /finngen/pipeline/cromwell/workflows/regenie/e76cf4f0-d5d0-49d6-98d6...

They will also appear as a job to the pipelines tool. Save your run pipeline ID from the pipelines tool front page. This is useful if you later wish to run, for example, a finemapping pipeline for those specific custom GWAS results. See also Tips on how to find a pipeline job ID.