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IGV is turning QUAL "." into -10 from this VCF of structural variations. I'm wondering if this means anything or if I should report a bug to the IGV devs.

Here's a row from a VCF:

#CHROM  POS ID  REF ALT QUAL    FILTER  INFO    FORMAT SAMPLE

chrY    11292098    DUP00008569 C   <DUP>   .   PASS    IMPRECISE;SVTYPE=DUP;SVMETHOD=EMBL.DELLYv0.8.1;CHR2=chrY;END=56834684;PE=3;MAPQ=24;CT=5to3;CIPOS=-265,265;CIEND=-265,265    GT:GL:GQ:FT:RCL:RC:RCR:CN:DR:DV:RR:RV0/1:-5.71458,0,-20.0913:57:PASS:0:90774:0:-1:6:5:0:0

You see the QUAL value is "."

IGV reports it as -10

igv screenshot

(This call is probably a false positive but it's just an example. There are others)

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Looks like they are treating the "." as a value of 1. According to the VCF spec the quality is "−10log10 prob". Where are you getting your QUALs from? I have never seen the quals as a "." and IGV probably needs to do some translation into an int but a QUAL of -10 makes no sense.

I would report it and let them explain.

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  • $\begingroup$ It's Delly structural variation caller, not a SNV caller so I guess the QUAL field wasn't what they wanted to use for quality of the call. Still IGV should just report a "." or nothing not some random negative value. $\endgroup$ – glyph May 29 '19 at 6:35
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    $\begingroup$ The QUAL field is often . when a quality couldn't be assigned. $\endgroup$ – terdon May 29 '19 at 9:08

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