How to run Conditional Analysis

Introduction

Conditional analyis is a GWAS tool that performs associations while conditioning over a set (one or more ) of initial variants. It is performed with REGENIE.

We provide the following tools

Unmodifiable Conditional Analysis Pipeline

This 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 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, but users can pass their own phenotype file and covariates, bypassing the checks/limitations required for automatic export.