# How to run Conditional Analysis

## Introduction

[Conditional analyis](https://docs.finngen.fi/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/). 

We provide the following tools 

## Unmodifiable Conditional Analysis Pipeline

This [pipeline ](https://docs.finngen.fi/working-in-the-sandbox/running-analyses-in-sandbox/how-to-run-genome-wide-association-studies-gwas/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 ](https://docs.finngen.fi/working-in-the-sandbox/running-analyses-in-sandbox/how-to-run-genome-wide-association-studies-gwas/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](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), but users can pass their own phenotype file and covariates, bypassing the checks/limitations required for automatic export.