Download Beagle 5.1. 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.
- Download Beagle 4.0 Mac Os
- Download Beagle 4.0 Mac Torrent
- Download Beagle 4.0 Machines
- Download Beagle 4.0 Machine
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Contents
Beagle 4.0 is not the current Beagle release
The current Beagle release can be found at http://faculty.washington.edu/browning/beagle/beagle.html.
Introduction
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:
- a standard format (Variant Call Format) for input and output files
- a powerful identity by descent detection algorithm: Refined IBD
- support for multi-threaded computation
- support for multi-allelic markers
- improved methods for phasing and genotype imputation
- elimination of temporary files
- use of a sliding window permit control memory use
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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Download Beagle 4.0
Download Beagle 4.0 Mac Os
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_4.0_06Jun17.pdf | Beagle version 4.0 documentation |
run.beagle.r1399.example | a unix script which runs a short Beagle analysis |
beagle4_release_notes | description of post-release changes in Beagle 4 |
gpl_license | GNU General Public License |
beagle.r1399.src.zip | source code for Beagle 4.0 (r1399) |
Download Beagle 4.0 Mac Torrent
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 |
Download Beagle 4.0 Machines
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Copyright: 2013-2018 Brian L. Browning
Last updated: 14 May 2018
Last updated: 14 May 2018