[BENCHMARK] dataset comparison igenvar only

[Irallia]

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.

Some of the example BAM files (all HG002) are aligned to different references:

    MtSinai_PacBio:     GCA_000001405.15_GRCh38_no_alt_analysis_set.fa
    PacBio_CCS_10kb:    hs37d5.fa
    10X_Genomics:       hg19.reordered.fa
    Illumina:           GCA_000001405.15_GRCh38_no_alt_plus_hs38d1_analysis_set.fa
    Illumina_Mate_Pair: GCA_000001405.15_GRCh38_no_alt_plus_hs38d1_analysis_set.fa

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.

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[Irallia]

Updated plots (GRCh37) DUPs as INS

[joshuak94]

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.