Beagle 4.0

Version: r1399
Email: browning@uw.edu

Contents

• Beagle 4.0 is not the current Beagle release
• Introduction
• Download Beagle 4.0

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.

back to contents

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

[ top ]

Download Beagle 4.0

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 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.

The following resources are also available:

[ top ]

Copyright: 2013-2018 Brian L. Browning
Last updated: 14 May 2018