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?