Hi there

I am interested in detecting structural rearrangements such as large insertions, deletion, inversion and translocation. I have found many different types of structural variations and I just want to make all these variation to be annotated and also in order to reduce the rearrangements variants size and prioritize variants , I have to go filtering process.

However well-known annotated program called ANNOVAR looks like fitting for SNPs and INDELs rather than structural rearrangements. Of course, not gene based , I mean that in case of filtered based, region based.

As a matter of fact, I already ran Annovar filter based and region based annotation but it didn't make any good results. (most of the result's file size is 0)

Therefore, I ask a few questions as follows :

1. Annovar doesn't fit for structural rearrangments in case of region based and filter based annotation. Right?
2. If so, How can I prioritize many variation from structural rearrangements variants calling program?