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

Abstract

Summary: 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.

Availability and implementation: 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/.