vcf2bed {bedr}

convert a vcf to a bed file

Description

Convert a vcf to a bed file. Currently, it needs to read into R via read.vcf

Usage

vcf2bed(x, filename = NULL, header = FALSE, other = NULL, verbose = TRUE)

Arguments

x

a vcf object

filename

the name of file if you want it exported

header

indicate if the bed file has header or not when exported

other

fields to include apart from chr, start, end.

verbose

more words

Value

A bed styled R object or an external file

Author(s)

Daryl Waggott

Examples

clinVar.vcf.example <- system.file("extdata/clinvar_dbSNP138_example.vcf.gz", package = "bedr")
x <- read.vcf(clinVar.vcf.example)
x.bed <- vcf2bed(x)