read_vcf: parses VCF into GRanges or data.table

In mskilab/skidb: Collection of R functions for accessing and parsing flat file dumps of common databases and external software used by @mskilab.

parses VCF into GRanges or data.table

Description

Wrapper around Bioconductor VariantAnnotation. Reads VCF into GRanges or data.table format

Usage

read_vcf(
  fn,
  gr = NULL,
  hg = "hg19",
  geno = NULL,
  swap.header = NULL,
  verbose = FALSE,
  add.path = FALSE,
  tmp.dir = "~/temp/.tmpvcf",
  ...
)

Arguments

fn	argument to parse via bcftools
gr	GRanges input GRanges (default = NULL)
hg	string Human reference genome (default = 'hg19')
geno	boolean Flag whether to pull the genotype information information in the GENO vcf fields (default = NULL)
swap.header	string Pathn to another VCF file (in case of VCF with malformed header)(default = NULL)
verbose	boolean Flag (default = FALSE)
add.path	boolean Flag to add the path of the current VCF file to the output (default = FALSE)
tmp.dir	string Path to directory for temporary files (default = '~/temp/.tmpvcf')
...	extra parameters

Author(s)

Marcin Imielinski

mskilab/skidb documentation built on Feb. 6, 2023, 2:49 a.m.