Difference between 0/0 and ./. for genotype in VCF

Question

[verne91]

What is the difference between 0/0 and ./. for a genotype in a VCF file?

Answer 1

[Ram]

Have you tried searching online for an answer? I googled "dot in GT field" and found this post as the second result: VCF file period symbol in the genotype

Also, the first link was to a VCF specification document (not the current version but that doesn't matter in this situation), which states very clearly:

GT : genotype, encoded as allele values separated by either of / or |. The allele values are 0 for the reference allele (what is in the REF field), 1 for the first allele listed in ALT, 2 for the second allele list in ALT and so on. For diploid calls examples could be 0/1, 1 | 0, or 1/2, etc. For haploid calls, e.g. on Y, male nonpseudoautosomal X, or mitochondrion, only one allele value should be given; a triploid call might look like 0/0/1. If a call cannot be made for a sample at a given locus, ‘.’ should be specified for each missing allele in the GT field (for example ‘./.’ for a diploid genotype and ‘.’ for haploid genotype).

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