Oh, I see now why I never had this problem. I always remove duplicate paired reads before SV detection (which is what the "d" means).
I can't recommend keeping duplicates in the files for SV analysis. Part of the robustness of SV detection is based on accurately counting the number of unique paired reads across a SV breakpoint. If you're leaving in duplicates, those numbers will be off and you'll potentially end up with additional false positives. A long mate-pair library should not have a large number of paired duplicates anyway unless the library was unfortunately low in complexity.
I can't recommend keeping duplicates in the files for SV analysis. Part of the robustness of SV detection is based on accurately counting the number of unique paired reads across a SV breakpoint. If you're leaving in duplicates, those numbers will be off and you'll potentially end up with additional false positives. A long mate-pair library should not have a large number of paired duplicates anyway unless the library was unfortunately low in complexity.
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