all these tracks are from the same human sample. There is a duplication called by Manta followed by a deletion called by a read-depth method. But the duplication actually have a copy-number of 2. So, it looks like, a large deletion happened first, then some sort of duplication (we see the signature of "green" paired reads there) which affected a part of deleted region (and thus it became a copy-number 2 again).
Did anyone see such "copy-number neutral duplication sharing a breakpoint with a deletion" thing? How could it be interpreted? How could it arose?