Regenie ​

Regenie 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 ​

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 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, where Regenie was first introduced.