The Bioinformatics & Genomics group together with the System Biology Group, at the Computer Science Dept. www.unito.it/di/, have recently published on Bioinformatics chimera, a tool for secondary analysis of fusion events.
Chimera is a Bioconductor package that organizes, annotates, analyses and validates fusions reported by different fusion detection tools; current implementation can deal with output from bellerophontes, chimeraScan, deFuse, fusionCatcher, FusionFinder, FusionHunter, FusionMap, mapSplice, Rsubread, tophat-fusion and STAR. The core of Chimera is a fusion data structure that can store fusion events detected with any of the aforementioned tools. Fusions are then easily manipulated with standard R functions or through the set of functionalities specifically developed in Chimera with the aim of supporting the user in managing fusions and discriminating false-positive results. Pubmed id: http://www.ncbi.nlm.nih.gov/pubmed/25286921