|Program:||beagle 5.1 (version: 18May20.d20)|
OS/2 Warp 4 incorporated a number of new technologies over OS/2 Warp 3, such as Java, OpenGL, OpenDoc, and VoiceType. It also updated the appearance of the Workplace Shell. Click here to download a simple shell script for dividing your sample. Two specialized programs, pseudomarker.jar and cluster2haps.jar are described in the BEAGLE documentation, and may be useful to some users: pseudomarker.jar - A utility program for creating a phased Beagle file of pseudomarkers from a Beagle output model (.dag) file. Global Nav Open Menu Global Nav Close Menu; Apple; Shopping Bag +.
Download Beagle Wallpapers for Android to the beagle is a breed of small hound that is similar in appearance to the much larger foxhound. Heimdall is an open source and cross platform utility that offers you the possibility to flash Samsung Galaxy devices. Keep in mind that flashing firmware to your mobile device is a potentially damaging practice, and that you will void your warranty, while possibly rendering your phone useless.
Download Beagle 4.0 Machines
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
Download Beagle 4.0 Machine
This reference will be updated when the Beagle version 5 phasing method is published.
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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.
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: May 18, 2020