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?
GQfield can be dropped from theFORMATfield, if I understood correctly. $\endgroup$.is what you put when one of the samples or alleles in the file is missing aGQvalue. Are you asking ifGQis a required field for a valid VCF file or if you can have a VCF withoutGQ? $\endgroup$GQequals theQUALfield of the variant, or if it's dropped because we only have one allele. $\endgroup$