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
- It is fast and memory efficient ๐ฅ
- For binary traits it supports Firth logistic regression and an SPA test
- It can perform gene/region-based burden tests
- 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
Full documentation for the regenie can be found here.
Mbatchou, J., Barnard, L., Backman, J. et al. Computationally efficient whole-genome regression for quantitative and binary traits. Nat Genet 53, 1097โ1103 (2021). https://doi.org/10.1038/s41588-021-00870-7
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.
Version 2.2.4 (Bug fix for multi-trait step 1 run with binary traits of different missingness patterns)
Version 2.2.3 (Bug fix for binary traits for which null logistic regression gives 0/1 fitted probabilities; enabled multi-threaded null model fitting for approximate Firth null models)
Version 2.2.2 (Bug fix for binary traits for which null logistic regression gives 0/1 fitted probabilities [i.e. highly imbalanced or low case counts]; New option --sex-specific
for sex-specific analyses)
Version 2.2.1 (Bug fix for Step 2 with binary traits for which null logistic regression gives 0/1 fitted probabilities [i.e. highly imbalanced or low case counts])
Version 2.2 (Faster implementation of Step 1 and 2 (see here for details); new options --write-null-firth/--use-null-firth
to store the estimates from approximate Firth null model; new option --minCaseCount
to filter out BTs with low number of cases from the analysis; new option --no-split
to enforce output of summary stats to a single file for all traits; added support for tranposed phenotype file format with --tphenoFile
)
Version 2.0.2 (Bug fix for burden testing with BGEN files not in v1.2 with 8-bit encoding; enabled faster step 2 implementation with Zstd compressed BGEN files in v1.2 with 8-bit encoding)
Version 2.0.1 (New option --catCovList
to specify categorical covariates; Enabled parameter expansion when specifying select phenotypes/covariates to analyze [e.g. 'PC{1:10}'])
Version 2.0 (Added burden testing functionality for region or gene-based tests [see website for details]; added sample size column in summary stats output).
For past releases, see here.