Program: BEAGLE
Version: 3.1.1
Copyright (c) 2007-2010 Brian L. Browning
Email: b.browning@auckland.ac.nz
This page was last updated on 5 January 2010
At the 2009 ASHG and IGES meetings I presented a new method for genotype calling for SNP arrays that can substantially reduce the number of false-positive associations caused by genotyping artifacts. This method is implemented in a new software package called BEAGLECALL and is described in the paper:
Browning B, Yu Z (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]
BEAGLE 3.1 extends BEAGLE to accept genotype likelihoods (rather than called genotypes) for unrelated individuals. Genotype likelihoods enable genotype uncertainty to be incorporated during phasing and imputation. Version 3.1 has a few additional small changes relative to version 3.0 that are described on the first page of the BEAGLE documentation. BEAGLE 3.1 requires Java version 1.6.
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 contents
If you use BEAGLE in a published analysis, please report the BEAGLE version used and cite the appropriate publication or publications given below.
Browning B, Yu Z (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]
A BEAGLE analysis of a large genome-wide association study is described in the following paper:
B L Browning and S R Browning (2008) Haplotypic analysis of Wellcome Trust Case Control Consortium data. Human Genetics 123:273-280. [link to article]
The preceding reference describes strategies for eliminating false-positive associations due to genotyping artefacts. However, in our experience, a much better way to eliminate false-positive associations due to genotyping artefacts is to simultaneously call and phase genotypes using BEAGLECALL prior to performing a haplotypic analysis using BEAGLE.
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:
The BEAGLE Utilities web site has a number of utility programs that can be used to prepare input files and process output files. Click here to visit the BEAGLE Utilities web site .
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.
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 program.
Two specialized programs, pseudomarker.jar and cluster2haps.jar, are described in the BEAGLE documentation, and may be useful to some users: