Beagle 5.4

Program: beagle 5.4 (version: 27May24.118)
Author: Brian Browning



Beagle is a software package for phasing genotypes and imputing ungenotyped markers. Beagle version 5.4 has improved memory and computational efficiency when analyzing large sequence data sets.

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If you use Beagle in a published analysis, please report the program version and cite the appropriate article.

The Beagle 5.4 genotype phasing method is described in:

B L Browning, X Tian, Y Zhou, and S R Browning (2021) Fast two-stage phasing of large-scale sequence data. Am J Hum Genet 108(10):1880-1890. doi:10.1016/j.ajhg.2021.08.005

The Beagle 5.4 genotype imputation method is described in:

B L Browning, Y Zhou, and S R Browning (2018). A one-penny imputed genome from next generation reference panels. Am J Hum Genet 103(3):338-348. doi:10.1016/j.ajhg.2018.07.015

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Download Beagle 5.4

Beagle is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.git

Beagle is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.

You can download a copy of the the GNU General Public License from

Source files in the net/sf/samtools/ directory are from the Broad Institute and are used to perform BGZIP compression and decompression. Source files from the Broad Institute are licensed under the MIT license.

beagle.27May24.118.jar Beagle 5.4 program file (requires Java version 8)
beagle_5.4_18Mar22.pdf Beagle 5.4 documentation
run.beagle.27May24.118.example a unix script which runs a short Beagle 5.4 analysis
beagle5_release_notes description of post-release changes in Beagle version 5
gpl_license GNU General Public License

The following resources are also available:

human genetic maps HapMap GrCh36, GrCh37, and GrCh38 genetic maps with cM units in PLINK format
human reference panel 1000 Genomes Project phase 3 reference panel
bref3.27May24.118.jar Converts from VCF format to bref3 format. Enter "java ‑jar bref3.27May24.118.jar help" for usage instructions
unbref3.27May24.118.jar Converts from bref3 format to VCF format. Enter "java ‑jar unbref3.27May24.118.jar help" for usage instructions
Variant Call Format An introduction to Variant Call Format (VCF)
conform-gt a program for making alleles in a VCF file consistent with a reference VCF file
Beagle Utilities a suite of utility programs
Beagle 5.3 the Beagle 5.3 web page
Beagle 5.2 the Beagle 5.2 web page
Beagle 5.1 the Beagle 5.1 web page
Beagle 4.1 the Beagle 4.1 web page
bref3.24May18.pdf The bref3 file format specification source code for Beagle 5.4 (27May24.118)

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Copyright: 2013-2024 Brian L. Browning
Last updated: May 27, 2024