Welcome to the Recalling Genotypes with BEAGLECALL Tutorial!ΒΆ


Updated: June 24th, 2014

Level: Advanced

Packages: SNP Analysis, Power Seat

BEAGLE and BEAGLECALL are Java-based tools for genetic analysis developed and maintained by Drs. Brian Browning and Sharon Browning of the University of Auckland. BEAGLE is particularly useful for inferring or imputing the genotypes of missing and untested SNPs. BEAGLECALL is a companion to BEAGLE that utilizes a combination of haplotype structure and allele intensity data to determine genotypes. This added data dimension results in very accurate genotype calls.

This tutorial focuses on BEAGLECALL showcasing add-on scripts required for importing and exporting back and forth between SVS to BEAGLECALL. It also provides a workflow to maximize the efficiency of these products. Many of the scripts featured in this tutorial can also be used with BEAGLE, which has the same file formats as BEAGLECALL.


To complete this tutorial you will need to download and unzip the following files, which includes several datasets.


The BEAGLE_Tutorial.zip file is large and may take awhile to download. Its main purpose is to help you follow along step-by-step. However, if you do not wish to download the file you can still use this tutorial as a general outline for your own study.

We hope you enjoy the experience and look forward to your feedback.