BEAGLE Genetic Analysis Software Package

Program: BEAGLE
Version: 3.3.2
Copyright (c) 2007-2011 Brian L. Browning
Email: browning@uw.edu
This page was last updated on 31 Oct 2011

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Postdoctoral Position

Applicants are invited for a postdoctoral position in the area of statistical genetics, with an emphasis on methods and analyses based on identity-by-descent.  Click here for more details.

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Introduction

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 can also be used in conjunction with PRESTO, a program for fast and flexible permutation testing. PRESTO can compute empirical distributions of order statistics, analyze stratified data, and determine significance levels for one-stage and two-stage genetic association studies.

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).

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New Features in BEAGLE 3.1, 3.2, and 3.3

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Citation

If you use BEAGLE in a published analysis, please report the BEAGLE version used and cite the appropriate publication or publications listed below.

  1. BEAGLE's fastIBD method is described in
    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]
  2. BEAGLE's methods for detecting homozygosity-by-descent and identity-by-descent are described in
    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]
  3. BEAGLE's methods for calling genotypes from genotype likelihood data are described in
    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]
  4. BEAGLE's methods for imputing ungenotyped markers and phasing parent-offspring trios are described in
    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]
  5. BEAGLE's methods for inferring haplotype phase or sporadic missing data in unrelated individuals are described in
    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]
  6. BEAGLE's methods for association testing are described in
    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]
  7. BEAGLE's haplotype frequency model was first described in:

    S R Browning (2006) Multilocus association mapping using variable-length Markov chains. Am J Hum Genet 78:903-13. [link to article]

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Download 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:

  1. beagle_3.3.2_31Oct11.pdf - The documentation for BEAGLE.
  2. beagle.jar - The BEAGLE executable file.
  3. beagle_example.zip - A ZIP-compressed directory with example input and output files from a BEAGLE analysis.  The analysis of the example files is described in the BEAGLE documentation.

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Download Phased Imputation Reference Panels

Phased genotype data in BEAGLE format from individuals sequenced by the 1000 Genomes Project (2010.11.23 sequence index) are available for download from

http://bochet.gcc.biostat.washington.edu/beagle/1000_Genomes.interim_phase1_release/

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Utility Programs

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:

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Version History

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Old Versions

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