This is interesting! It makes sense that pacbio CCS reads are much easier to call SVs from: they have long read lengths and relatively high accuracy. However, it is a bit concerning that just illumina mate-pair reads result in such low accuracy. I'd be curious to see how this looks specifically with something like Deletions, since deletions can be detected somewhat robustly just via read-depth.
Maybe if we can find out if there is a specific variant which is bringing the whole curve down, we can better understand what the issue there is.
https://github.com/seqan/iGenVar/pull/201#issuecomment-1105146893: