I called structure variant using Sniffles for two samples (using PacBio reads), I would like  to compare the resulted two files to know what is common and different in both files.

what first come to my mind is to use vcf-isec, but I do not know how it will deal with the deletion size if they are exist in the two files but different in length for example, translocation also if its origin is the same but the location transferred to is different!  etc .. 

vcf-compare could be used but I do not know if it is the right way!

is there is a tool that could do this in an efficient way? anyone have experience with that?

Thanks,
One simple way to do this is to merge the SV calls and look at which calls collapse. I've writing some code to do this in VCF format. 

https://github.com/zeeev/mergeSVcallers
