I have structural calls represented in bedpe format http://bedtools.readthedocs.org/en/latest/content/general-usage.html#bedpe-format
I want to merge the calls with both ends overlapping. similar to this question Merging And De-Duplicating Structural Variant Calls (Bedpe)
and it seems to be not an easy job.
Anyone has written tools for this kind of task?
I am aware of svtools https://github.com/hall-lab/svtools, but it is still under development, and not tested yet.