regenie
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 handle population structure and relatedness
- It can process multiple phenotypes at once efficiently
- For binary traits, it supports Firth logistic regression and an SPA test
- It can perform gene/region-based tests (Burden, SBAT, SKAT/SKATO, ACATV/ACATO)
- It can perform interaction tests (GxE, GxG) as well as conditional analyses
- Meta-analysis of REGENIE summary statistics can be performed using REMETA
- 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)
- It can be installed with Conda
Citation
Mbatchou, J., Barnard, L., Backman, J. et al. Computationally efficient whole-genome regression for quantitative and binary traits. Nat Genet 53, 1097–1103 (2021). https://doi.org/10.1038/s41588-021-00870-7
License
regenie is distributed under an MIT license.
Contact
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.