BEAGLE is a software program for imputing genotypes, inferring haplotype phase, and performing genetic association analysis. BEAGLE is designed to analyze large-scale data sets with hundreds of thousands of markers genotyped on thousands of samples. BEAGLE can

• phase genotype data (i.e. infer haplotypes) for unrelated individuals, parent-offspring pairs, and parent-offspring trios.
• infer sporadic missing genotype data.
• impute ungenotyped markers that have been genotyped in a reference panel.
• perform single marker and haplotypic association analysis.

Beagle was developed by Brian Browning at the University of Washington.

• Beagle Main Site: Beagle at Univ. of Washington

• Module Name: Beagle (see the modules page for more information)
• Multithreaded
• Unusual environment variables set:
  • $BEAGLEDIR Beagle installation directory
  • $BEAGLE_JAR path to the Beagle jar file
• Example files in $BEAGLEDIR

Allocate an interactive session and run the program. Sample session:

[user@biowulf]$ sinteractive --cpus-per-task=8 --mem=8g
salloc.exe: Pending job allocation 46116226
salloc.exe: job 46116226 queued and waiting for resources
salloc.exe: job 46116226 has been allocated resources
salloc.exe: Granted job allocation 46116226
salloc.exe: Waiting for resource configuration
salloc.exe: Nodes cn3144 are ready for job

[user@cn3144 ~]$ module load Beagle
[user@cn3144 ~]$ java -jar $BEAGLE_JAR nthreads=$SLURM_CPUS_PER_TASK gt=test.08Jun17.d8b.vcf.gz out=out.gt
beagle.08Jun17.d8b.jar (version 4.1)
Copyright (C) 2014-2015 Brian L. Browning
Enter "java -jar beagle.08Jun17.d8b.jar" for a summary of command line arguments.
Start time: 10:15 AM EDT on 31 Aug 2017

Command line: java -Xmx27305m -jar beagle.jar
  nthreads=8
  gt=test.08Jun17.d8b.vcf.gz
  out=out.gt

No genetic map is specified: using 1 cM = 1 Mb

reference samples:       0
target samples:        191

[ ... ]

Number of markers:                1356
Total time for building model: 6 seconds
Total time for sampling:       8 seconds
Total run time:                15 seconds

End time: 10:15 AM EDT on 31 Aug 2017
beagle.08Jun17.d8b.jar (version 4.1) finished
user@cn3144 ~]$
[user@cn3144 ~]$ exit
salloc.exe: Relinquishing job allocation 46116226
[user@biowulf ~]$

Create a batch input file (e.g. Beagle.sh). For example:

#!/bin/bash
module load Beagle
java -jar $BEAGLE_JAR nthreads=$SLURM_CPUS_PER_TASK gt=test.08Jun17.d8b.vcf.gz out=out.gt

Submit this job using the Slurm sbatch command.

sbatch [--cpus-per-task=#] [--mem=#] Beagle.sh