vcf2bedpe {bedr} | R Documentation |
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)
[Package bedr version 1.1.3 Index]