harmonize: The harmonization of SNP identifiers and alleles.

In GWAtoolbox: GWAS Quality Control

Description

Function harmonizes SNP identifiers and alleles in the input file according to the provided VCF reference.

Usage

harmonize(input, output, vcf, chromosome = "chr", id = "markername", alleles = c("ref_allele", "non_ref_allele"), sep = "\t", vcf_alleles = TRUE, drop = FALSE, gzip = TRUE)

Arguments

input	Name of an input file.
output	Name of an output file.
vcf	Name of the VCF reference.
chromosome	Name of the column containing chromosome names in the specified input file.
id	Name of the column containing SNP identifiers in the specified input file.
alleles	Vector with column names containing reference and non-reference alleles in the specified input file.
sep	The field separator character in the specified input file.
vcf_alleles	When applicable, alleles in the input file are recoded to R(reference)/I(insertion)/D(deletion) format. If vcf_alleles is set to TRUE, then alleles are recoded based on the VCF reference. Otherwise, alleles are recoded using only information available in the input file.
drop	If TRUE, then all unresolved variants are dropped from the output file.
gzip	TRUE if output file is in gzip format.

Author(s)

Daniel Taliun, Christian Fuchsberger, Cristian Pattaro

GWAtoolbox documentation built on May 2, 2019, 4:54 p.m.