regenie 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
- For binary traits it supports Firth logistic regression and an SPA test
- It can perform gene/region-based burden tests
- It is fast and memory efficient 🔥
- It supports the BGEN, PLINK bed/bim/fam and PLINK2 pgen/pvar/psam genetic data formats
- It is ideally suited for implementation in Apache Spark (see GLOW)
Citation Joelle Mbatchou, Leland Barnard, Joshua Backman, Anthony Marcketta, Jack A. Kosmicki, Andrey Ziyatdinov, Christian Benner, Colm O'Dushlaine, Mathew Barber, Boris Boutkov, Lukas Habegger, Manuel Ferreira, Jeffrey Reid, Goncalo Abecasis, Evan Maxwell, Jonathan Marchini. (2020) Computationally efficient whole genome regression for quantitative and binary traits [BioRxiv pre-print]
regenie is distributed under an MIT license.
If you have any questions about regenie please contact
If you want to submit a issue concerning the software please do so using the regenie Github repository.