# How to run Conditional Analysis

## Introduction

[Conditional analyis](../../../background-reading/conditional-analysis) 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/).&#x20;

We provide the following tools&#x20;

## Unmodifiable Conditional Analysis Pipeline

This [pipeline ](conditional-analysis/unmodifiable-conditional-analysis-pipeline)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 ](conditional-analysis/unmodifiable-conditional-analysis-custom-regions-pipeline)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](conditional-analysis/modifiable-conditional-analysis-custom-regions-pipeline), but users can pass their own phenotype file and covariates, bypassing the checks/limitations required for automatic export.&#x20;
