How can I call structural variants (SVs) from pair-end short read resequencing data?
I think the best method or combination of methods will depend on aspects of the data that might vary from one dataset to another. E.g. the type, size, and frequency of structural variants, the number SNVs, the quality of the reference, contaminants or other issues (e.g. read quality, sequencing errors) etc.

For that reason, I'd take two approaches:


Try a lot of methods, and look at their overlap
Validate a subset of calls from different methods by wet lab experiments - in the end this is the only real way of knowing the accuracy for a particular case.