http://jewmanchue.github.io/wham/
WHole-genome Alignment Metrics (WHAM) is a structural variant (SV) caller that integrates several sources of mapping information to identify SVs. WHAM classifies SVs using a flexible and extendable machine-learning algorithm (random forest). WHAM is not only accurate at identifying SVs, but its association test can identify shared SVs enriched in a cohort of diseased individuals compared to a background of healthy individuals.
WHAM can be easily run as a stand alone tool or as part of gkno (http://gkno.me) or bcbio-nextgen (http://bcbio-nextgen.readthedocs.org) pipelines.
Currently we are preparing the WHAM manuscript. If you would like to use and cite this tool, for the time being, please cite the WHAM github page.