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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 🔥
• 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, 1097–1103 (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

• [email protected]
• [email protected]

If you want to submit a issue concerning the software please do so using the regenie Github repository.

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.