Closed Irallia closed 2 years ago
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Updated plots (GRCh37)
DUPs as INS
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.
UPDATE: look at the new plots below.
In this plot you can see the results of iGenVar with 2 short read and 3 long read sets and their combinations.
Since the truth set does not contain DUPs, I created another plot where all DUPs are interpreted as INS.
The important question now is, are most sets really that bad, or does iGenVar simply not find SVs. This I want to find out in comparison with other callers.