UpdateVCF: Update genotypes of vcf file

In inzilico/imputeqc: A Quality Control for Genotype Imputation

Description

Update GT fields of vcf file by haplotypes provided. Updated file is saved under the name, which can be numbered to distinguish files in a set. It is useful, when you create a set of vcf files where GT fields are masked in different ways. These files will be further imputed. The updated genotypes are written as unphased.

Usage

UpdateVCF(haps, pref, n, vcf)

Arguments

haps	character vector with haplotypes
pref	path/to/pref, where 'pref' is a basename of output file. vcf extention is added.
n	ordinal number to mark updated files automatically. If provided, m followed by this number is added to the basename of the file.
vcf	vcf-class object loaded with readVcf() function from VariantAnnotation package. The genotypes of this object we want to update.

inzilico/imputeqc documentation built on July 28, 2020, 5:31 p.m.