gt2refalt: Two-letter genotype from VCF GT
In Tmisc: Turner Miscellaneous

gt2refalt

R Documentation

Two-letter genotype from VCF GT

Description

Get a two-letter genotype from a VCF GT field. Current implementation is quick and dirty, and only accepts 0/0, 0/1, or 1/1. Any other input to gt will return a missing value.

Usage

gt2refalt(gt, ref, alt)

Arguments

`gt`	The genotype field (must be 0/0, 0/1, or 1/1).
`ref`	The reference allele.
`alt`	The alternate allele.

Value

Returnvalue

Examples

gt2refalt(gt="0/0", ref="R", alt="A")
gt2refalt(gt="0/1", ref="R", alt="A")
gt2refalt(gt="1/1", ref="R", alt="A")
gt2refalt(gt="0/2", ref="R", alt="A")
gt2refalt(gt="./.", ref="R", alt="A")

Tmisc documentation built on Aug. 23, 2023, 1:07 a.m.