Beagle version 4.1

Program: beagle.09Feb16.2b7.jar
Author: Brian Browning



Beagle is a software package that performs genotype calling, genotype phasing, imputation of ungenotyped markers, and identity-by-descent segment detection.

Beagle version 4.1 has a more accurate genotype phasing algorithm and a very fast and accurate genotype imputation algorithm. Version 4.1 also has several changes to the command line arguments which are described in the release notes. The "ped" argument has no effect in version 4.1. If your data contains nuclear families and you want to model the parent-offspring relationships when phasing genotypes, please use version 4.0.

If you use Beagle 4.1 in a published analysis, please report the program version and cite the appropriate article.

The citation for Beagle's phasing algorithm 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

The citation for Beagle's genotype imputation algorithm is:

B L Browning and S R Browning (2016). Genotype imputation with millions of reference samples. Am J Hum Genet 98:116-126. doi:10.1016/j.ajhg.2015.11.020

The citation for Beagle's IBD detection algorithm is:

B L Browning and S R Browning (2013). Improving the accuracy and efficiency of identity-by-descent detection in population data. Genetics 194(2):459-71. doi:10.1534/genetics.113.150029

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Download Beagle 4.1

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 the 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.09Feb16.2b7.jar Beagle program file (requires Java version 8)
beagle_4.1_09Feb16.pdf Beagle version 4.1 documentation
run.beagle.09Feb16.2b7.example a unix script which runs a short Beagle analysis
release_notes description of changes in recent versions
gpl_license GNU General Public License source code for Beagle 4.1 (09Feb16.2b7)

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
bref.09Feb16.2b7.jar a program for compressing diploid reference VCF files. Enter "java -jar bref.09Feb16.2b7.jar" for program documentation.
bref.16Dec15.pdf The bref file format specification.
version 4.0 the Beagle version 4.0 web page
version 3 the Beagle version 3 web page

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Copyright: 2013-2016 Brian L. Browning
Last updated: 09 February 2016