Regenie

Regenie (opens new window) is a C++ program for whole genome regression modelling of large genome-wide association studies. Regenie is developed and supported by a team of scientists at the Regeneron Genetics Center.

• Properties
• Requirements
• Installation
• Genome-wide association analysis

Properties

The method has the following properties:

• It works on quantitative and binary traits, including binary traits with unbalanced case-control ratios
• It can process multiple phenotypes at once
• It is fast and memory efficient
• For binary traits it supports Firth logistic regression and an SPA test
• It supports the BGEN, PLINK bed/bim/fam and PLINK2 pgen/pvar/psam genetic data formats

Requirements

Requirements

• Conda (miniconda), see our Conda tutorial for more details.
• Conda channels: conda-forge, bioconda

You will need bioconda and conda-forge channels. If you have not set channels yet make sure to add them in this order:

conda config --add channels bioconda
conda config --add channels conda-forge

Installation

Install regenie into your environment:

conda install -c bioconda regenie

Genome-wide association analysis

We recommend Regenie documentation (opens new window) to read up on gwas analysis using Regenie. For more details we recommend having a look on the official paper Computationally efficient whole genome regression for quantitative and binary traits (opens new window), where Regenie was first introduced.