VCF File type

Question

[khatami.mahshid]

Hi all,

I have VCF File for all chromosomes. I wonder if any of SNPs in these chromosomes have groups except 0/0-0/1-1/0-1/1?

thanks

Answer 1

[manuel.belmadani]

That group is called the "genotype", and yes, you could have 2 or higher if there's 2 or more non-reference alleles, and you can have a pipe | instead of / if the genotype is phased.

GT genotype, encoded as alleles values separated by either of ”/” or “|”, e.g. The allele values are 0 for the reference allele (what is in the reference sequence), 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 or 1|0 etc. For haploid calls, e.g. on Y, male X, mitochondrion, only one allele value should be given. All samples must have GT call information; if a call cannot be made for a sample at a given locus, ”.” must be specified for each missing allele in the GT field (for example ./. for a diploid).

The meanings of the separators are: / : genotype unphased | : genotype phased

See the VCF spec: http://www.internationalgenome.org/wiki/Analysis/vcf4.0/