Program: BEAGLE
Version: 3.3.2
Copyright (c) 2007-2013 Brian L. Browning
Email: browning@uw.edu
This page was last updated on 29 Sep 2014
The current Beagle release can be found at http://faculty.washington.edu/browning/beagle/beagle.html.
BEAGLE is a state of the art software package for analysis of large-scale genetic data sets with hundreds of thousands of markers genotyped on thousands of samples. BEAGLE can
BEAGLE is written in Java and runs on any computing platform with a Java version 1.6 interpreter (e.g. Windows, Unix, Linux, Solaris, Mac).
back to contentsIf you use BEAGLE version 3 in a published analysis, please report the BEAGLE version used and cite the appropriate publication or publications listed below.
B L Browning and S R Browning (2011) A fast, powerful method for detecting identity by descent. The American Journal of Human Genetics 88:173-182. [link to article]
S R Browning and B L Browning (2010) High-resolution detection of identity by descent in unrelated individuals. The American Journal of Human Genetics 86:526-539. [link to article]
B L Browning and Z Yu (2009) Simultaneous genotype calling and haplotype phase inference improves genotype accuracy and reduces false positive associations for genome-wide association studies. The American Journal of Human Genetics 85:847-861. [link to article]
B L Browning and S R Browning (2009) A unified approach to genotype imputation and haplotype phase inference for large data sets of trios and unrelated individuals. Am J Hum Genet 84:210-223. [link to article]
S R Browning and B L Browning (2007) Rapid and accurate haplotype phasing and missing data inference for whole genome association studies using localized haplotype clustering. Am J Hum Genet 81:1084-1097. [link to article]
B L Browning and S R Browning (2007) Efficient multilocus association mapping for whole genome association studies using localized haplotype clustering. Genet Epidemiol 31:365-375. [link to article]
S R Browning (2006) Multilocus association mapping using variable-length Markov chains. Am J Hum Genet 78:903-13. [link to article]
You may download and use the BEAGLE executable file for non-commercial and commercial research. BEAGLE is distributed on an "AS IS" basis. There is NO WARRANTY for the program, to the extent permitted by applicable law. In no event unless required by applicable law will any BEAGLE copyright holder be liable to you for damages, including any general, special, incidental or consequential damages arising out of the use or inability to use the program (including but not limited to loss of data or data being rendered inaccurate or losses sustained by you or third parties or a failure of the program to operate with any other programs).
The following files are available for download:
Phased genotype data in BEAGLE format from phase 1 of the 1000 Genomes Project are available for download from
http://bochet.gcc.biostat.washington.edu/beagle/1000_Genomes.phase1_release_v3/
The BEAGLE Utilities web site has a number of utility programs that can be used to prepare input files and process output files.
When using multiple Beagle input files, the alleles for a marker must be on the same chromosome strand in each input file. Sharon Browning has written a python script that checks that alleles are defined with respect to the same chromosome strand and switches alleles if necessary to make the chromosome strands consistent. Click here to download Sharon's strand-checking utility.
Sharon Browning has written some utilities for processing output files from BEAGLE HBD/IBD analysis. Click here to download Sharon's HBD/IBD utilities.
When dealing with large sample sizes, it might be necessary to divide a sample so that imputation can be performed in each subsample separately. Click here to download a simple shell script for dividing your sample.
Two specialized programs, pseudomarker.jar and cluster2haps.jar are described in the BEAGLE documentation, and may be useful to some users: