Body: <p>I cannot find in the <a href="https://samtools.github.io/hts-specs/VCFv4.3.pdf" rel="nofollow noreferrer">VCF specs</a> what is the default value of Genotype Quality <code>GQ</code> for haploid calls. In such case, is the default the missing value <code>.</code>?</p>
  <p>From the specs:</p>
  <blockquote>
  <p>If any of the fields is missing, it is replaced with the MISSING value. For example if the FORMAT is GT:GQ:DP:HQ
  then 0 | 0 : . : 23 : 23, 34 indicates that GQ is missing. If a field contains a list of missing values, it can be represented
  either as a single MISSING value (‘.’) or as a list of missing values (e.g. ‘.,.,.’ if the field was Number=3). Trailing
  fields can be dropped, with the exception of the GT field, which should always be present if specified in the FORMAT
  field.</p>
  </blockquote>
  <p>From this I assume that there is no default value, <code>GQ</code> might be dropped from the <code>FORMAT</code> field, correct?</p>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2021-10-06T13:56:00.620Z
Comments.Text: Can you give an example? Why would there be a default quality?
Comments.UserDisplayName: terdon
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2021-10-06T17:10:00.160Z
Comments.Text: Thanks @terdon, I probably misread the specs. I updated the post with a part of the specs that indicates the `GQ` field can be dropped from the `FORMAT` field, if I understood correctly.
Comments.UserDisplayName: gc5
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2021-10-06T17:13:08.510Z
Comments.Text: Thanks, but I'm still a bit confused. You are already quoting the relevant section that explains that yes, `.` is what you put when one of the samples or alleles in the file is missing a `GQ` value.  Are you asking if `GQ` is a required field for a valid VCF file or if you can have a VCF without `GQ`?
Comments.UserDisplayName: terdon
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2021-10-06T19:46:19.413Z
Comments.Text: Sure. My doubt derives from the fact that I haven't understood if, for haploid calls, the `GQ` equals the `QUAL` field of the variant, or if it's dropped because we only have one allele.
Comments.UserDisplayName: gc5
Tags: <vcf><genotyping>
Title: Genotype quality in VCF for haploid calls
ThreadText: # Genotype quality in VCF for haploid calls
  
  (Asked by: username_0 on 2021-10-05)
  
  I cannot find in the [VCF specs](https://samtools.github.io/hts-specs/VCFv4.3.pdf) what is the default value of Genotype Quality `GQ` for haploid calls. In such case, is the default the missing value `.`?
  
  From the specs:
  
  > If any of the fields is missing, it is replaced with the MISSING value. For example if the FORMAT is GT:GQ:DP:HQ
  > then 0 | 0 : . : 23 : 23, 34 indicates that GQ is missing. If a field contains a list of missing values, it can be represented
  > either as a single MISSING value (‘.’) or as a list of missing values (e.g. ‘.,.,.’ if the field was Number=3). Trailing
  > fields can be dropped, with the exception of the GT field, which should always be present if specified in the FORMAT
  > field.
  
  From this I assume that there is no default value, `GQ` might be dropped from the `FORMAT` field, correct?
  
  **Tags:** vcf, genotyping
  
  > **Comments:**
  > **username_1**: Can you give an example? Why would there be a default quality?  
  > **username_0**: Thanks @username_1, I probably misread the specs. I updated the post with a part of the specs that indicates the `GQ` field can be dropped from the `FORMAT` field, if I understood correctly.  
  > **username_1**: Thanks, but I'm still a bit confused. You are already quoting the relevant section that explains that yes, `.` is what you put when one of the samples or alleles in the file is missing a `GQ` value.  Are you asking if `GQ` is a required field for a valid VCF file or if you can have a VCF without `GQ`?  
  > **username_0**: Sure. My doubt derives from the fact that I haven't understood if, for haploid calls, the `GQ` equals the `QUAL` field of the variant, or if it's dropped because we only have one allele.  
  
  ---
  
  ## 0 answers
  
  