Answers.Body: <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>
  
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Answers.CreationDate: 2019-05-29T06:35:42.537Z
Answers.Text: 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.
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Answers.Text: The QUAL field is often `.` when a quality couldn't be assigned.
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Body: <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>
  
Tags: <vcf><variant-calling><igv>
Title: Why does IGV turn a VCF QUAL of "." into -10?
ThreadText: # 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   <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](https://i.sstatic.net/oAXiB.png)](https://i.sstatic.net/oAXiB.png)
  
  (This call is probably a false positive but it's just an example. There are others)
  
  **Tags:** vcf, variant-calling, igv
  
  
  ---
  
  ## 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.  
  
  ---
  
  