> 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.md).

# How to run Conditional Analysis

## Introduction

[Conditional analyis](/background-reading/conditional-analysis.md) is a GWAS tool that performs associations while conditioning over a set (one or more ) of initial variants. It is performed with [REGENIE](https://rgcgithub.github.io/regenie/).

We provide the following tools

## Unmodifiable Conditional Analysis Pipeline

This [pipeline ](/working-in-the-sandbox/running-analyses-in-sandbox/how-to-run-genome-wide-association-studies-gwas/conditional-analysis/unmodifiable-conditional-analysis-pipeline.md)receives as inputs sumstats, nulls, pheno/cov file for a phenotype, finemaps the input sumstats to return the set of initial hits and performs iterative conditional analysis for each of the hits until a threshold is reached (either pval or # of hits).

## Unmodifiable Conditional Analysis Custom Regions Pipeline

[Pipeline ](/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)that is conceptually similar, but in this case no finemapping is done and the user must provide a file containing the hits (1 or more) and regions.

## Modifiable Conditional Analysis Custom Regions Pipeline

[Similar as above](/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), but users can pass their own phenotype file and covariates, bypassing the checks/limitations required for automatic export.


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