Beagle 5.0

Contents

• Beagle 5.0 is not the current Beagle release
• Introduction
• Citation
• Download Beagle 5.0

Beagle 5.0 is not the current Beagle release

The current Beagle release can be found at http://faculty.washington.edu/browning/beagle/beagle.html.

Introduction

Beagle is a software package for phasing genotypes and for imputing ungenotyped markers. Version 5.0 has new, fast algorithms for genotype phasing and imputation.

Version 5.0 has several changes to the command line arguments which are described in the Beagle 5.0 documentation and release notes. Refined IBD is now a stand-alone program, and is not part of Beagle 5.0. The "ped" argument has no effect in version 5.0. The most recent version of Beagle that models parent-offspring relationships is version 4.0. Beagle 5.0 does not infer genotypes from genotype likelihood data, but versions 4.0 or 4.1 can be used for this purpose.

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Citation

If you use Beagle 5.0 in a published analysis, please report the program version and cite the appropriate article.

The Beagle 5.0 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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Download Beagle 5.0

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.

The following resources are also available:

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Copyright: 2013-2019 Brian L. Browning
Last updated: August 12, 2019