> For the complete documentation index, see [llms.txt](https://docs.finngen.fi/llms.txt). Markdown versions of documentation pages are available by appending `.md` to page URLs; this page is available as [Markdown](https://docs.finngen.fi/working-in-the-sandbox/running-analyses-in-sandbox/how-to-run-genome-wide-association-studies-gwas/conditional-analysis/modifiable-conditional-analysis-custom-regions-pipeline.md).

# Modifiable Conditional Analysis Custom Regions Pipeline

## Summary

This pipeline is completely identical to the [unmodifiable version](/working-in-the-sandbox/running-analyses-in-sandbox/how-to-run-genome-wide-association-studies-gwas/conditional-analysis/unmodifiable-conditional-analysis-custom-regions-pipeline.md). The only difference here is an extra (optional) input:

* `conditional_analysis_custom.cov_file` Path to covariate file

\
These results will not be automatically exported