BEAGLECALL Genetic Analysis Software Package

Version: 1.0.1
Copyright (c) 2009-2010 Brian L. Browning
This page was last updated on 15 Nov 2010



BEAGLECALL is a software package for simultaneous genotype calling and haplotype phasing for unrelated individuals.  BEAGLECALL produces output posterior genotype probabilities and output phased haplotypes.  BEAGLECALL generates extremely accurate genotype calls because it uses both allele signal intensity data and inter-marker correlation to call genotypes.  BEAGLECALL is designed for use with high-density SNP arrays, and it uses the BEAGLE haplotype frequency model to model inter-marker correlation. 

If genotype call errors or false-positive associations caused by genotyping artefacts are complicating your analysis, try calling your genotypes using BEAGLECALL. 

BEAGLECALL is written in Java and runs on most computing platforms (e.g. Windows, Unix, Linux, Solaris, Mac).

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If you use BEAGLECALL in a published analysis, please report the version used and please cite the following article which describes BEAGLECALL's algorithms:

Browning B, Yu Z.  (2009)  Simultaneous genotype calling and haplotype phase inference improves genotype accuracy and reduces false positive associations for genome-wide association studies.    The American Journal of Human Genetics 85:847-861. [link to article]

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You may download and use the BEAGLECALL executable file for non-commercial and commercial research purposes.  The BEAGLECALL source code that is available for download is licensed under the Apache License, Version 2.0.  You may not use BEAGLECALL except in compliance with the License. You may obtain a copy of the License at

BEAGLECALL is distributed on an "AS IS" BASIS,  WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.   See the License for the specific language governing permissions and limitations under the License.

The following files are available for download:

  1. beaglecall_1.0_15Nov10.pdf - the documentation for BEAGLECALL.
  2. beaglecall.jar  - the BEAGLECALL executable file
  3. - a ZIP-compressed directory with with example input and output files from a BEAGLECALL analysis.
  4. - source code for BEAGLECALL (does not include source code for BEAGLE).  

There are also utility programs that can be used to prepare input and process output files for BEAGLECALL and BEAGLE.  These utility programs can be downloaded from the BEAGLE Utilities web site.

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BEAGLECALL Version History

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