Beagle version 4

Version: r1274



Beagle version 4 performs genotype calling, genotype phasing, imputation of ungenotyped markers, and identity-by-descent segment detection. Version 4 does not perform association testing, but version 3 can be used for this purpose.

Version 4 has multiple improvements:

If you use Beagle 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

You may download and use the Beagle 4 executable file for non-commercial and commercial research. Beagle is distributed on an "AS IS" basis. There is NO WARRANTY for the program, to the extent permitted by applicable law. In no event unless required by applicable law will any Beagle copyright holder be liable to you for damages, including any general, special, incidental or consequential damages arising out of the use or inability to use the program (including but not limited to loss of data or data being rendered inaccurate or losses sustained by you or third parties or a failure of the program to operate with any other programs).

b4.r1274.jar Beagle version 4 java executable
b4.03May14.pdf Beagle version 4 documentation
run.b4.r1274.example a unix script which runs a short Beagle analysis

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 1 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

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Copyright: 2013-2014 Brian L. Browning
Last updated: 03 May 2014