How to run survival analysis using GATE unmodifiable pipeline

How to run survival analysis using GATE unmodifiable pipeline

Unmodifiable pipelines are predefined workflows that cannot be modified by the user. Advantage of running unmodifiable pipelines compared to modifiable pipelines is that you will get results directly to the green library and the User results PheWeb browser. No download requests are needed, because results of unmodifiable pipeline have been verified not to contain any individual-level data.

Running the GATE unmodifiable pipeline is very similar to running GATE in regular pipelines, with just a few small changes. The unmodifiable GATE pipeline can be accessed in the sandbox from

The workflow for running the pipeline is: First, prepare a phenotype file for your endpoint. The phenotype file should contain the columns FID and IID for FINNGENIDs, as well as the endpoint column and its survivaltime column. This file does not have to contain covariates. See How to run GWAS using GATE (survival models) for more information.

Second, create a file with phenotype description(s), one per row. These will be when/if the endpoint will be uploaded to the userresults browser.

Third, fill in the input json in the unmodifiable pipeline json: gate.phenolist: A comma-separated list of your endpoints. Example value: "endpoint1,endpoint2" gate.phenodescriptionlist: The phenotype description file you created in the second step. gate.pheno_file: The phenotype file you created in the first step. gate.cov_file: If you do not have any newly-created covariates in your own covariate file, you do not need to edit this. Otherwise, put your covariate file here. gate.covariates: The covariates used in the analysis are given here, as a comma-separated list.

The results will be automatically copied to the User results PheWeb browser and the green library bucket specific for each data release: /finngen/library-green/finngen_R[RELEASE]/unmodifiable_pipelines/UnmodifiableGATEDF[RELEASE]/workflow_id E.g. for R12, to /finngen/library-green/finngen_R12/unmodifiable_pipelines/UnmodifiableGATEDF12/workflow_id. The workflow_id will be the pipelines app ID for your job.