Interpreting Mako breakpoints

[crohlicek]

Hello,

I'm hoping to include Mako in a benchmark of complex SV callers (see previous issue) and would like to make sure that Mako outputs are properly parsed. We're encountering frequent cases in which multiple intervals are reported within a single output SV call; however, their breakends do not align/match. For example, the following prediction was made at the site of a dDUP:

chr1 51362377 51517994 DEL,DUP ARP_Span;ARP_Self cxs=12;DUP,51362465-51517994,sa=0,rp=79;BND,51362377-51489365,sa=3,rp=30;DEL,51362387-51489264,sa=9,rp=0 ARP_LARGE_INSERT,SM,MS,ARP_RF,ARP_LARGE_INSERT,SM,ARP_LARGE_INSERT<>ARP_RF,ARP_LARGE_INSERT,MS 67+0-,22+23-,17+19-,0+79-,0+86-,17+12-,0+66-,80+0-,86+0-,23+27-

How should I interpret the breakpoints in this record given that the none of the breakpoints of the BND, DEL, and DUP intervals align with one another?

Thank you!