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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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 http://www.gnu.org/licenses/.
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|
|beagle.r1399.src.zip||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