Beagle version 4.0

Version: r1399


Beagle 4.0 is not the current Beagle release

The current Beagle release is version 4.1. Version 4.1 has a more accurate genotype phasing method and a much faster genotype imputation method. If your data contains nuclear families and you want to model the parent-offspring relationships when phasing genotypes, then you should use version 4.0 which can be downloaded from this web page.

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Beagle version 4.0 performs genotype calling, genotype phasing, imputation of ungenotyped markers, and identity-by-descent segment detection.

Version 4.0 includes several new features:

If you use Beagle 4.0 in a published analysis, please report the program version and cite the following article:

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 81:1084-97. doi:10.1086/521987

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Download Beagle 4.0

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 using a link provided below. If not, see

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.r1399.jar Beagle executable jar file (requires Java SE version 7)
beagle.03Mar15.pdf Beagle version 4.0 documentation
run.beagle.r1399.example a unix script which runs a short Beagle analysis
release_notes description of new features in recent versions
gpl_license GNU General Public License source code for Beagle 4.0 (r1399)

The following resources are also available:

human genetic maps HapMap GrCh36 and GrCh37 genetic maps in PLINK format for use with Refined IBD
human reference panel 1000 Genomes Project phase 3 reference panel.
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
version 3 the Beagle version 3 web page

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Copyright: 2013-2015 Brian L. Browning
Last updated: 08 September 2015