New Add-on Scripts Available: BEAGLE & BEAGLECALL Scripts Package

         September 8, 2010

In the ongoing quest to empower our customers with the latest in genetic analysis methods, we are continually releasing new functionality for SNP & Variation Suite 7 in the form of add-on scripts. Add-on scripts are written in Python, a clear and powerful object-oriented programming language similar to Java or Perl. Python provides fully-programmatic access to most aspects of the software making it easy for us and our customers to implement new methods, automate workflows and interact with other programs, and then to provide the new functionality to colleagues in a point-and-click interface.

Each month we’ll be highlighting new scripts that we’ve made available on our Add-on Scripts Repository. Every script can be downloaded and installed for free!

BEAGLE and BEAGLECALL Script Package
This month, we’ve released new scripts that make it easier to interact with BEAGLE and BEAGLECALL given the interest generated by a blog post by Dr. Bryce Christensen. BEAGLE is particularly useful for inferring or imputing genotypes of missing and untested SNPs. BEAGLECALL is a companion to BEAGLE that we have found to be the most accurate genotype calling tool available today.

The package includes:

  • Import BEAGLE
  • Import BEAGLE gprobs as Allelic Dosage
  • Export BEAGLE File (for targeted regions only)
  • Export BEAGLE by Chromosome
  • Export BEAGLECALL Genotype Probabilities
  • Export BEAGLECALL Allele Signals

Download the scripts here

As a compliment to these scripts we’ve also posted a step-by-step tutorial on how to get your data ready for BEAGLECALL in SVS.

Share your scripts with the research community
If you have written any scripts and think they are useful to others, we encourage you to share them with the community. Just email a *.txt or *.py file to with any accompanying documentation or special instructions. Once we test your script and check its validity, we’ll post it on our Add-on Scripts Repository for others to download.

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