I cannot find in the VCF specs 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?

  • $\begingroup$ Can you give an example? Why would there be a default quality? $\endgroup$
    – terdon
    Oct 6, 2021 at 13:56
  • $\begingroup$ 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. $\endgroup$
    – gc5
    Oct 6, 2021 at 17:10
  • $\begingroup$ 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? $\endgroup$
    – terdon
    Oct 6, 2021 at 17:13
  • $\begingroup$ 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. $\endgroup$
    – gc5
    Oct 6, 2021 at 19:46


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