How to run trajGWAS

What?

Pipeline for running GWAS for longitudinal trajectories (eg. multiple lab measurements per person) using TrajGWAS.

Introduction

Example files for running TrajGWAS pipeline

Example files for running trajGWAS pipeline can be found in the sandbox from folder /finngen/library-green/scripts/trajGWAS/:

• trajgwas.wdl

• trajgwas_example.json (example inputs)

Minimally, you need to create your phenotype-covariate file ("trajGWAS.gwas.phenofile"), which should be tab-separated file, including phenotype column (defined in "trajGWAS.phenoname") , all covariate columns (defined in "trajGWAS.gwas.covarlist" as a + separated list, NO SPACES).

How to submit your job

Using Pipelines

See How to use the Pipelines area to see how to submit your job.

If you need further information on the pipeline/job system, see section Pipelines is based on Cromwell and WDL.

Once your .json file is ready, you can submit your GATE run via the command:

finngen-cli request-workflow --wdl /path/to/trajgwas.wdl \
    --input /path/to/trajgwas_example.json

After submitting your job successfully, go to Applications->Sandbox->Pipelines to track your job, and remember to save your jobs' workflow ID for tracking and checking the results when your run has finished.

Output

Once your job displays the Succeeded state you can see the results in /finngen/pipeline/cromwell/workflows/trajGWAS/[WORKFLOW_ID]/.

You can, for example, find the:

• summary statistics ({PHENO}.trajGWAS.gz ) in /finngen/pipeline/cromwell/workflows/trajGWAS/[WORKFLOW_ID]/call-gather/shard-0/glob*/ and

• manhattan and QQ plots for both beta and tau p-values in the other glob* folder: /finngen/pipeline/cromwell/workflows/trajGWAS/[WORKFLOW_ID]/call-gather/shard-0/glob*/.