ReadVCF: ReadVCF

In cgab-ncc/FIREVAT: FIREVAT, FInding REliable Variants without ArTifacts

ReadVCF

Description

Reads a .vcf file

Usage

ReadVCF(
  vcf.file,
  genome = "hg19",
  split.info = FALSE,
  check.chromosome.name = TRUE,
  match.bsg = FALSE
)

Arguments

vcf.file	(full path of a .vcf file)
genome	A genome name for BSgenome (default: hg19)
split.info	A boolean value. If TRUE, then makes the INFO column in the vcf as a separate column. Default value is FALSE.
check.chromosome.name	A boolean value. If TRUE, then check whether converts
match.bsg	A boolean value. If TRUE, check whether chromosome matches with those in BSgenome 'MT' to 'M' and adds 'chr' to the CHROM column. Default value is TRUE.

Value

A list with elements 'data', 'header', 'genome'

cgab-ncc/FIREVAT documentation built on Nov. 19, 2022, 5:55 p.m.