<p>Looks like they are treating the "." as a value of 1.  According to the <a href="http://samtools.github.io/hts-specs/VCFv4.2.pdf" rel="nofollow noreferrer">VCF spec</a> 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. </p>

<p>I would report it and let them explain.</p>

CC BY-SA 4.0
2019-05-29T06:35:42.537Z
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.
111
CC BY-SA 4.0
2019-05-29T09:08:11.603Z
The QUAL field is often `.` when a quality couldn't be assigned.
terdon
CC BY-SA 4.0
2019-05-29T02:40:01.703Z
2019-05-29T02:40:01.703Z
Bioathlete
<p>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.</p>

<p>Here's a row from a VCF:</p>

<pre><code>#CHROM  POS ID  REF ALT QUAL    FILTER  INFO    FORMAT SAMPLE

chrY    11292098    DUP00008569 C   &lt;DUP&gt;   .   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
</code></pre>

<p>You see the QUAL value is "."</p>

<p>IGV reports it as -10</p>

<p><a href="https://i.sstatic.net/oAXiB.png" rel="nofollow noreferrer"><img src="https://i.sstatic.net/oAXiB.png" alt="igv screenshot"></a></p>

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

<vcf><variant-calling><igv>
Why does IGV turn a VCF QUAL of "." into -10?
# Why does IGV turn a VCF QUAL of "." into -10?

(Asked by: username_0 on 2019-05-29)

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      .   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

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

**Tags:** vcf, variant-calling, igv

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## 1 answers

### Answer by username_1 on 2019-05-29. Score: 3

Looks like they are treating the "." as a value of 1. According to the [VCF spec](http://samtools.github.io/hts-specs/VCFv4.2.pdf) 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.

> **Comments:**
> **username_0**: 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.  
> **username_2**: The QUAL field is often `.` when a quality couldn't be assigned.  

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