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