harmonize_by_pos: 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_by_pos(input, output, vcf, id = "markername", chromosome = "chr", position="position", alleles = c("first_allele", "second_allele"), flip = TRUE, sep = "\t", drop = FALSE, gzip = TRUE)

Arguments

input	Name of an input file.
output	Name of an output file.
vcf	Name of the VCF reference.
id	Name of the column containing SNP identifiers in the specified input file.
chromosome	Name of the column containing chromosome names in the specified input file.
position	Name of the column containing chromosomal positions in the specified input file.
alleles	Vector with column names containing first and second alleles in the specified input file.
flip	If TRUE, automatically flips alleles in order to match variant strand in VCF reference. Otherwise, the variant is considered as unresolved.
sep	The field separator character in the specified 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.