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.
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.