I don't know how people usually further filter structural variations, after making callings using multiple softwares (Pindel, CNVnator, Delly, Breakdancer, StriP.....you name it) ?
I'd like further prioritize those supported (reciprocal 70%) by at least two softwares. Does that sound reasonable? Intuitively I think so because SV identifications are still very noisy and technologically very challenging compared to SNP calling. I also saw some paper did the same (http://www.nature.com/articles/srep18501). But if I'm correct, in 1000Genome Project they "merged" to come up with a union based on output from 9 algorithms.
I proposed the above to my professors (they are geneticists but not bioinformaticians, basically have zero knowledge about NGS-based SV calling) and they thought "supported by at least two softwares" or "70% reciprocal overlap" are simply too arbitrary. How would I explain and convince them? Personally I think lots of procedures in SV calling and filter are indeed very arbitrary given the complex nature of structural variation and challenge for NGS-based calling.