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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.
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#201 (comment):
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