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 Auckland, NZ. Beagle website.
Sample session (user input in bold). This run uses the sample data in /usr/local/beagle/example/imputation/
helix% java -Xmx4000m -jar /usr/local/beagle/beagle.jar markers=hapmap.markers phased=hapmap.phased.bgl unphased=hapmap.unphased.bgl missing=? out=test Beagle version 3.3.2 (31 Oct 2011) Enter "java -jar beagle.jar" for summary of command line arguments. Start time: 01:07 PM EDT on 24 Jul 2012 Command line: java -Xmx3555m -jar beagle.jar markers=hapmap.markers phased=hapmap.phased.bgl unphased=hapmap.unphased.bgl missing=? out=test number of markers = 100 number of haplotypes = 4 (hapmap.unphased.bgl) number of haplotypes = 116 (hapmap.phased.bgl) Phasing: iteration 1 Phasing: iteration 2 Phasing: iteration 3 Phasing: iteration 4 Phasing: iteration 5 Phasing: iteration 6 Phasing: iteration 7 Phasing: iteration 8 Phasing: iteration 9 Phasing: iteration 10 Running time for phasing: 0 seconds Beagle version 3.3.2 (31 Oct 2011) finished
This example runs Beagle using the sample data, and limits it to 4000 Mb. You should not use more than 100 GB of memory on Helix.
If you expect to use Beagle frequently, it will be convenient to set up an alias as below:
Bash users: add this to your /home/user/.bashrc file
alias beagle='java -Xmx4000m -jar /usr/local/beagle/beagle.jar'
tcsh/csh users: add this to your /home/user/.cshrc file
alias beagle 'java -Xmx4000m -jar /usr/local/beagle/beagle.jar'
You will then be able to run Beagle by typing a command like:
helix% beagle markers=hapmap.markers phased=hapmap.phased.bgl unphased=hapmap.unphased.bgl missing=? out=test