Conditional analysis

What?

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

Example files:

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

• conditional_analysis.wdl and input files (needs to be edited):

• conditional_analysis_DF10.json ,

• conditional_analysis_DF11.json and

• conditional_analysis_DF12.json

This example is for running conditional GWAS using regenie for endpoint T1D in DF10m DF11 and DF12, respectively.

Define your Inputs

In the .json, ihese 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

• regenie_cond_sb.regenie_conditional.null_root: Root for your GWAS null model file (.loco.gz). If you have run your GWAS using regenie pipeline, you can find your null model files under step1 outputs.

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_DF12.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/regenie_conditional_sb/[WORKFLOW_ID]/