Example of genotype information:
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 non-pseudoautosomal 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). The meanings of the separators are as follows (see the PS field below for more details on incorporating phasing information into the genotypes)
The allele balance (fraction of ref bases over ref + alt bases) across all bialleleic het-called samples
The depth of coverage of each VCF allele in this sample.
Conditional genotype quality, encoded as a phred quality -10log_10p(genotype call is wrong, conditioned on the site's being variant) (Float)
The phred-scaled genotype likelihoods rounded to the closest integer (and otherwise defined precisely as the GL field) (Integers)