Beagle is a software package that performs genotype calling, genotype phasing, imputation of ungenotyped markers, and identity-by-descent segment detection.

Version: 4.1

Availability: MARCONI

Target: all

Official web site:

Related Commands:

Beagle is distributed as a .jar file. The current version (4.1)

requires Java 8.

To run beagle 4.1, load the jre module and the beagle module 

  $ module load jre

  $ module load beagle/4.1

and then run

  $ java -jar $BEAGLE_HOME/beagle-4.1.jar

Running the jar without parameters will print a list of all the