# Causeway: a pipeline for genome-wide effector gene screening with Mendelian Randomization and colocalization

## TL;DR

Causeway is a new pipeline that efficiently identifies causal genes using Mendelian Randomization and colocalization, even on low-resource computers.

## Contribution

Causeway introduces a scalable and computationally efficient pipeline for genome-wide causal gene screening.

## Key findings

- Causeway performs two-sample Mendelian Randomization using summary statistics for gene prioritization.
- The pipeline includes sensitivity and colocalization analyses to ensure robust results.
- It is designed to work efficiently on personal computers and scale to high-performance clusters.

## Abstract

The integration of quantitative trait loci and disease genome-wide association studies for pinpointing candidate causal genes is a computationally demanding task accompanied by pitfalls related to the methods used. To address these issues, we introduce Causeway, a novel Nextflow pipeline for performing summary statistics-based two sample Mendelian Randomization for causal gene prioritization. The pipeline executes sensitivity and colocalization analyses for interrogation of findings providing robust results. The tool is designed to run tasks in a computationally efficient way even in low-resource environments, such as a personal computer. Furthermore, it can scale to web servers and high-performance computing clusters.

The source code of Causeway is available at GitHub https://github.com/juliaapolonio/Causeway, while the documentation and instructions to run the vignette at https://juliaapolonio.github.io/Causeway/.