VCF - genotypes - "missing alleles"

[Elsie]

Hi, according to the VCF specifications for Genotype fields:
"”.” must be specified for each missing allele in the GT field (for example ./. for a diploid)."
What is a missing allele?, how does it happen? My colleague believes that they occur when the variant caller has too little information and refuses to make any call at all (say, zero coverage), but we'd like to know for sure why they appear.

Many thanks.

[Bukowski]

In a multisample VCF file they will represent positions where the genotype of the variant is unknown, but known in other samples. This could be due to lack of coverage. But you need some way to flag something that is 'missing'.

[Elsie]

Thanks, that is useful. We are working with multisample VCF files.