2
$\begingroup$

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)

Improve this question
$\endgroup$

1 Answer 1

Reset to default
3
$\begingroup$

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.

Improve this answer
$\endgroup$
2
  • $\begingroup$ 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. $\endgroup$
    – 111
    Commented May 29, 2019 at 6:35
  • 1
    $\begingroup$ The QUAL field is often . when a quality couldn't be assigned. $\endgroup$
    – terdon ♦
    Commented May 29, 2019 at 9:08

Your Answer

By clicking “Post Your Answer”, you agree to our terms of service and acknowledge you have read our privacy policy.

Not the answer you're looking for? Browse other questions tagged or ask your own question.