Custom GWAS CLI Quantitative mode

From the Sandbox (v10.2 onwards) the Custom GWAS CLI is available in binary mode and quantitative mode for the REGENIE pipeline. 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.

Note: Please be conscious of how many runs you generate while using this method. If you are going to launch more than 5 GWASs at the same time please contact the [e-mail] and we can temporarily increase the resources of your organization's Sandbox and downscale afterward. Submitting too many GWASs with default settings can make your organization's pipeline unusable for others.

For instructions on how to use the method, enter the following command in a terminal:

finngen-cli request-gwas --help

Running Custom GWAS in Quantitative mode

To run Custom GWAS in quantitative mode, create a phenotype file with two tab-separated columns. In the first column, paste your FinnGen IDs, and in the second column your continuous variable value. Column headings are expected by default.

Example phenofile is as follows:

FID	CONTINUOSX
FG00000001	0.878979
FG00000002	0.862703
FG00000003	0.0387807
FG00000004	0.4239
FG00000005	0.445
FG00000006	0.0766014
FG00000007	0.361489
FG00000008	0.738852
FG00000009	0.124793

And some example code to run the quantitative custom GWAS - CLI tool:

finngen-cli request-gwas \
--phenotype-name CONTINUOSX \
--analysis-description test_run \
--bin false \
--phenofile /path/to/phenofile.tsv \
--notification-email [e-mail] \
--release finngen_R9

Note:

• When using a phenofile the phenotype name value must match the phenotype column header ("CONTINUOUSX" as in the above column header of the file, and in the command that is used to launch the GWAS)

• Phenotype name must be all caps

• Phenotype must ne numerical (for example 1E-5 notation not allowed)

• When running quantitative GWAS, set --bin parameter to false, as in the example above

Similarly to binary phenotypes, you can set the analysis type (--analysistype) to additive, recessive, or dominant depending on the model you like to use. If you don't select anything (as in the exampel above) the Custom GWAS CLI will be run under the additive model (default).

When your GWAS-CLI run has been successfully submitted, you should see the following messages in the terminal:

You can also check the status of your run from the custom GWAS tool RECENTS menu.

Custom GWAS results tables

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/.

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 after --phenotype-name (e.g. CONTINUOSX in the example above). 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 additionally saved in the Cromwell jobs directory in Sandbox: /finngen/pipeline/cromwell/workflows/[workflow_name]/[workflow_ID].

They will also appear as a job in the pipelines tool. Save your run ID from the pipelines tool's 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.