Genal: A Python Toolkit for Genetic Risk Scoring and Mendelian Randomization

Abstract

Here we present Genal, a python module for population genetic analyses. It includes functionalities for cleaning and formatting Single Nucleotide Polymorphism (SNP)-level data, clumping, lifting, SNP association testing, polygenic risk scoring, and mendelian randomization analyses, all within a single module. It was designed with user-friendliness in mind, aiming to reduce the programming skills threshold required for medical scientists to perform genetic epidemiology studies. Genal eliminates the need to interact with the command line and switch between multiple R packages with different requirements, making it considerably more accessible to a wide range of researchers. Genal draws on concepts from several well-established tools, ensuring that users have access to rigorous statistical techniques in the intuitive Python environment.