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.
bedpe files are just two bed files linked together. It is like two linked GRanges, maybe bioc development team can develop a higher data structure for this type of data.
rtracklayer may include bedpe format. Not sure what's the status now.
I am also aware of GenomicInteraction bioc package, but it does not have the function I want to use for my purpose.
Thank you very much!