vcf2bedpe: convert a vcf to a bedpe file

In bedr: Genomic Region Processing using Tools Such as 'BEDTools', 'BEDOPS' and 'Tabix'

convert a vcf to a bedpe file

Description

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

Usage

vcf2bedpe(x, filename = NULL, header = FALSE, verbose = TRUE)

Arguments

x	a vcf object
filename	the name of the output bedpe file, if NULL then bedpe is not exported
header	indicate if the bed file has header or not when exported
verbose	detailed messages

Value

A bedpe styled R object or an external file

Author(s)

Helena Winata

Examples

gridss.vcf.example <- system.file("extdata/gridssSV.vcf.gz", package = "bedr")
x <- read.vcf(gridss.vcf.example, split.info = TRUE)
x.bedpe <- vcf2bedpe(x)

bedr documentation built on April 11, 2025, 5:52 p.m.