Table of Contents

• Introduction
• Running WHAM and WHAMG on Breezy

Introduction

WHAM and WHAMG are programs for structural variant detection in DNA sequences.  The WHAM/WHAMG web site suggests that WHAMG, rather than the older WHAM package should be used in most cases.

Running WHAM and WHAMG on Breezy

The binaries for the software have been installed under /global/software/wham/wham170/bin.  The license agreement is in the directory /global/software/wham/wham170.

The wham and whamg binaries were built with OpenMP parallel processing support.  The number of threads used should match the number of cores requested of the batch job system (with a TORQUE directive of the form #PBS -l nodes=1:ppn=n) by setting the OMP_NUM_THREADS environment variable to ${PBS_NUM_PPN}.  So, for example, to run WHAMG, use:

export OMP_NUM_THREADS=${PBS_NUM_PPN}
/global/software/wham/wham170/bin/whamg <command line options>