For this paper An integrated map of structural variation in 2,504 human genomes my tiny part was to validate complex structural variation in long read TruSeq data.
It was about 3 years ago so I'm not sure if there are better approaches. But we created breakpoint contigs across putative SV breakpoints using Velvet.
Then I took the breakpoint contigs (there are many possible ones generated by Velvet) and I used BLAT to align them to the reference genome.
Using the BLAT results I was able to parse out the precise breakpoints.
Like I said it's rather labor intensive and I'm sure there's a better way of doing it. But this might be a good lead!