Conditional analysis

Pipeline for running conditional GWAS (conditioned on the lead variant of some genome-wide significant loci) using regenie and DF10.

Example files:

Example files for running conditional pipeline can be found in sandbox under folder /finngen/library-green/scripts/conditional/:

• conditional_analysis.wdl and

• conditional_analysis.json (inputs, needs editing)

This example is for running conditional GWAS using regenie for endpoint T1D in DF10.

Define your Inputs

In the .json, these are some parameters you most probaply want to edit:

• regenie_cond_sb.pheno: name of the phenotype to run the analysis. This pipeline can be only run for one phenotype at a time.

• regenie_cond_sb.chroms: list of chromosomes to run the analyses for. Convenient if you know you have hit only in some chromosomes. In the example, all chromosomes (1-22+X) are listed

• regenie_cond_sb.filter_covariates.covariates: List of covariates to be used in the model

Submit your job

Once your inputs are in order, you can submit your job via command line:

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

REMEMBER to save your job ID [WORKFLOW_ID]to keep track of your job and to be able to view the output! See also tips on how to find a pipeline job ID. The [WORKFLOW_ID] and your job can be monitored from the pipelines.

Output

Once your job is Succeeded, you can find your ouput from the folder /finngen/pipeline/cromwell/