<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>

CC BY-SA 4.0
2021-10-06T13:56:00.620Z
Can you give an example? Why would there be a default quality?
terdon
CC BY-SA 4.0
2021-10-06T17:10:00.160Z
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.
gc5
CC BY-SA 4.0
2021-10-06T17:13:08.510Z
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`?
terdon
CC BY-SA 4.0
2021-10-06T19:46:19.413Z
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.
gc5
<vcf><genotyping>
Genotype quality in VCF for haploid calls
# 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 @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.  
> **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.  

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## 0 answers

