Beagle

Introduction

Beagle is a software package for phasing genotypes and for imputing ungenotyped markers. Start it with: beagle [java options] [arguments] Note: Bref is not installed in this container.

For more information, please check its website: https://biocontainers.pro/tools/beagle and its home page: https://faculty.washington.edu/browning/beagle/beagle.html.

Versions

5.1_24Aug19.3e8

Commands

beagle

Module

You can load the modules by:

module load biocontainers
module load beagle

Example job

Warning

Using #!/bin/sh -l as shebang in the slurm job script will cause the failure of some biocontainer modules. Please use #!/bin/bash instead.

To run Beagle on our clusters:

#!/bin/bash
#SBATCH -A myallocation     # Allocation name
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 1
#SBATCH --job-name=beagle
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out

module --force purge
ml biocontainers beagle

beagle gt=test.vcf.gz out=test.out