Beagle 5.0

Program: beagle.12Jul19.jar
Author: Brian Browning


Beagle 5.0 is not the current Beagle release

The current Beagle release can be found at


Beagle is a software package for phasing genotypes and for imputing ungenotyped markers. Version 5.0 has new, fast algorithms for genotype phasing and imputation.

Version 5.0 has several changes to the command line arguments which are described in the Beagle 5.0 documentation and release notes. Refined IBD is now a stand-alone program, and is not part of Beagle 5.0. The "ped" argument has no effect in version 5.0. The most recent version of Beagle that models parent-offspring relationships is version 4.0. Beagle 5.0 does not infer genotypes from genotype likelihood data, but versions 4.0 or 4.1 can be used for this purpose.

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If you use Beagle 5.0 in a published analysis, please report the program version and cite the appropriate article.

The Beagle 5.0 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

The most recent reference for Beagle's phasing method is:

S R Browning and B L Browning (2007) Rapid and accurate haplotype phasing and missing data inference for whole genome association studies by use of localized haplotype clustering. Am J Hum Genet 81:1084-1097. doi:10.1086/521987

This reference will be updated when the Beagle version 5 phasing method is published.

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Download Beagle 5.0

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.

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.12Jul19.jar Beagle 5.0 program file (requires Java version 8)
beagle_5.0_03Jul19.pdf Beagle 5.0 documentation
run.beagle.12Jul19.example a unix script which runs a short Beagle 5.0 analysis
beagle5_release_notes description of post-release changes in Beagle 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
bref3.12Jul19.jar Converts from VCF format to bref3 format. Enter "java ‑jar bref3.12Jul19.jar help" for usage instructions
unbref3.12Jul19.jar Converts from bref3 format to VCF format. Enter "java ‑jar unbref3.12Jul19.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 to be consistent with a reference VCF file
Beagle Utilities a suite of utility programs
Beagle 4.1 the Beagle 4.1 web page
Beagle 4.0 the Beagle 4.0 web page
bref3.24May18.pdf The bref3 file format specification source code for Beagle 5.0 (12Jul19)

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Copyright: 2013-2019 Brian L. Browning
Last updated: August 12, 2019