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Workflow's Outputs

The workflow generates a (potentially large) number of results files that can be a bit difficult to navigate at first.

The results of the main workflow are:

  • The GWAS summary statistics, formatted as GROUP_NAME.PHENOTYPE.gwas.tsv. One for each group and phenotype.
  • The GWAS plots, formatted as GROUP_NAME.PHENOTYPE.PLOT_TYPE.png. One for each group, phenotype and plot type (currently QQ, Manhattan).
  • The finemapping summary statistics, formatted as GROUP_NAME.PHENOTYPE.finemapping.tsv. One for each group and phenotype.
  • Optional locus plots, formatted as GROUP_NAME.PHENOTYPE.LEAD_VARIANT_ID.locuszoom.png. One for each group, phenotype and locus passing the fine-mapping thresholds.

If no groups are provided, the groupname is set to GROUP_NAME=all. Otherwise, and if the meta-analysis stage was requested, the following outputs will be created.

  • Meta-Analysed GWAS results, formatted as META_ANALYSIS.PHENOTYPE.gwas.tsv. One for each phenotype.
  • Meta-Analysed GWAS plots, formatted as META_ANALYSIS.PHENOTYPE.PLOT_TYPE.png. One for each phenotype and plot type (currently QQ, Manhattan).
  • Meta-Analysis based finemapping results, formatted as META_ANALYSIS.PHENOTYPE.finemapping.tsv. One for each phenotype.
  • Optional meta-analysis based locus plots, formatted as META_ANALYSIS.PHENOTYPE.LEAD_VARIANT_ID.locuszoom.png. One for each phenotype and locus passing the finemapping thresholds.

All results are found in the output folder whose lcoation and organisation depend on the execution engine.

Local Execution with Cromwell

The outputs will be stored in the output folder defined by the final_workflow_outputs_dir variable specified in the cromwell's option file. The output folder is typically organised in subfolders corresponding to the workflow's tasks.

For example, for a grouped analysis with meta-analysis you should have the following subfolders:

  • call-gwas_group_plots: Containing plots for each analysed group.
  • call-gwas_meta_plots: Containing the plots for the meta-analysis.
  • call-merge_gwas_group_chr_results: Containing GWAS results for each group.
  • call-meta_analyse: Containing meta-analysed GWAS results.
  • call-merge_fp_group_chr_results: Containing finemapping results for each group.
  • call-merge_fp_meta_chr_results: Containing finemapping results from the meta-analysis stage using summary statistics.

UK Biobank RAP

In that case, the output folder is defined by the destination argument provided to dx run. Results will be found as a flat list in the output folder and all intermediate results are stored in the intermediate subfolder.