Structural variant detection and association testing
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All WHAM documents can be found on the wiki:

What is 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 ( or bcbio-nextgen ( 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.