bedr (version 1.1.3)

vcf2bedpe: 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)

Value

A bedpe styled R object or an external file

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

Author

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)