This is a pretty complex question, but detection usually depends on clever ways of aligning your sequence to the reference genome and then fishing for events that are not 'normal', i.e. all those that can only be explained by fusion events etc...

I don't know of any dedicated (Perl) code for this, but perl is certainly capable of doing the filtering.

You might be better asking at a more specific forum e.g. seqAnswers or cruising the literature on pubmed.

Happy hunting!