GT Style Genotype

This algorithm uses the numeric genotype field to create a representation with the allele bases.

Requirements

• 0/1 Genotypes Field: The imported variants must have a numeric sample genotype field (0/1).

Options

• Golden Helix ‘G_T’: This option will create a genotype field with the represented alleles separated with an underscore. The alleles are sorted lexicographically before they are joined.
• VCF encoding ‘G/T’: This option will create a genotype field with the represented alleles separated by a backslash (or a pipe ‘|’ for phased genotypes). The alleles will appear in the order that their indexes appear in the original numeric Genotype field.

Output

A Genotype column is created containing a text representation of the genotype. This column will be appended to the variant sample fields.