| Program: | beagle 5.1 (version: 18May20.d20) |
| Author: | Brian Browning |
| Email: | browning@uw.edu |
The current Beagle release can be found at http://faculty.washington.edu/browning/beagle/beagle.html.
Beagle is a software package for phasing genotypes and for imputing ungenotyped markers. Beagle 5.1 is similar to version 5.0, but includes some additional improvements that increase accuracy and reduce computation time.
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If you use Beagle in a published analysis, please report the program version and cite the appropriate article.
The Beagle 5.1 genotype imputation method is described in:
B L Browning, Y Zhou, and S R Browning (2018). A one-penny imputed genome from next generation reference panels. Am J Hum Genet 103(3):338-348. doi:10.1016/j.ajhg.2018.07.015
The most recent reference for Beagle's phasing method is:
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 81:1084-1097. doi:10.1086/521987
This reference will be updated when the Beagle version 5 phasing method is published.
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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 from 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.18May20.d20.jar | Beagle 5.1 program file (requires Java version 8) |
| beagle_5.1_08Nov19.pdf | Beagle 5.1 documentation |
| run.beagle.18May20.d20.example | a unix script which runs a short Beagle 5.1 analysis |
| beagle5_release_notes | description of post-release changes in Beagle version 5 |
| gpl_license | GNU General Public License |
The following resources are also available:
| human genetic maps | HapMap GrCh36, GrCh37, and GrCh38 genetic maps with cM units in PLINK format |
| human reference panel | 1000 Genomes Project phase 3 reference panel |
| bref3.18May20.d20.jar | Converts from VCF format to bref3 format. Enter "java ‑jar bref3.18May20.d20.jar help" for usage instructions |
| unbref3.18May20.d20.jar | Converts from bref3 format to VCF format. Enter "java ‑jar unbref3.18May20.d20.jar help" for usage instructions |
| Variant Call Format | An introduction to Variant Call Format (VCF) |
| 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 |
| Beagle 5.0 | the Beagle 5.0 web page |
| Beagle 4.1 | the Beagle 4.1 web page |
| Beagle 4.0 | the Beagle 4.0 web page |
| bref3.24May18.pdf | The bref3 file format specification |
| beagle.200518.zip | source code for Beagle 5.1 (18May20.d20) |
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Copyright: 2013-2020 Brian L. Browning
Last updated: Apr 21, 2021