Difference between revisions of "FreeBayes"
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Revision as of 16:30, 10 August 2012
Description
FreeBayes is a high-performance, flexible, and open-source Bayesian genetic variant detector. It operates on BAM alignment files, which are produced by most contemporary short-read aligners.
In addition to substantial performance improvements over its predecessors (PolyBayes, GigaBayes, and BamBayes), it expands the scope of SNP and small-indel variant calling to populations of individuals with heterogeneous copy number. FreeBayes is currently under active development.
Execution Environment and Modules
To use freebayes with the environment modules system at HPC the following commands are available:
Get module information for freebayes:
$module spider freebayes
Load the default application module:
$module load freebayes
The modulefile for this software adds the directory with executable files to the shell execution PATH and sets the following environment variables:
- HPC_FREEBAYES_DIR - directory where freebayes is located.
- HPC_FREEBAYES_BIN - executable directory