writeVcf: Write VCF file

In jmonlong/PopSV: Population-based detection of structural variants from Read-Depth signal

Description

Transforms the BED/data.frame format into a VCF format and write a VCF file. The calls are merged if they have exactly the same coordinates ('chr', 'start' and 'end').

Usage

writeVcf(cnv.df, output.file = "cnvs.vcf",
  genome = BSgenome.Hsapiens.UCSC.hg19::BSgenome.Hsapiens.UCSC.hg19)

Arguments

cnv.df	the data.frame with the cnv calls (from 'call.abnormal.cov').
output.file	the file name for the output VCF file. Default is 'cnvs.vcf'
genome	BSgenome to retrieve REF nucleotide. Default is hg19 (BSgenome.Hsapiens.UCSC.hg19::Hsapiens).

Value

the output file name.

Author(s)

Jean Monlong

jmonlong/PopSV documentation built on Sept. 15, 2019, 9:29 p.m.