lmerge/ prune workflow still results in overlapping calls

[djakubosky]

Just wanted to bring up that running lsort/lmerge/prune pipeline seems to still result in a number of overlapping calls (>50% Reciprocal overlap for about 1000 variant pairs in my filtered call-set). I am curious as to if this behavior is expected. They don't tend to have similar AF (which is probably why they aren't merged but I am have been taking the set of breakpoints with the highest AF and removing others as my solution for now.

Let me know if you have any thoughts, Thanks!

[djakubosky]

I wanted to add in this example as something I wouldn't expect after merging or pruning

this particular variant is found in mostly the same individuals, and overlaps >50%

[jxcao98]

Hello, I have met the same problem, have you found the answer?