(2) Very often in the NAIBR output, I see SVs with a lot of split-molecules (high-score) but without any discordant read pairs. But I am sure from generating my candidates, that there are often plenty discordant reads around the breakpoint. This is not really a big problem for me, the SV call and orientation usually seems right, and I get that there are surely differences in calling the discordant read pairs. But I am asking myself: How does NAIBR infer the SVs orientation, if it didn't find any discordant reads? The orientation is often right, so maybe that's just a bug in the output?
TDLR: Why is there candidate SV with zero reported discordant reads
See discussion in #10
TDLR: Why is there candidate SV with zero reported discordant reads