FreeBayes

Overview

• FreeBayes: a haplotype-based variant detector.

Using

Use the module name freebayes to discover versions available and to load the application.

Module loading freebayes also loads the following applications: bc, parallel, samtools and vcftools. To see the specific versions type ml from the command line.

Additional scripts can be found and downloaded from freebayes/scripts

Multicore:

The freebayes command itself does not run across multiple cores.

But “in general, freebayes can be parallelised by running multiple instances of freebayes on separate regions of the genome, and then concatenating the resulting output. The wrapper, freebayes-parallel will perform this, using GNU parallel.“ A version of parallel is included within the module load.