vcf2vranges: Load a VCF file
In daewoooo/StrandPhaseR: Phase template strands from Strand-seq data

vcf2vranges

R Documentation

Load a VCF file

This function loads raw VCF file into a VRanges-class object.

vcf2vranges(
  vcfFile = NULL,
  genoField = NULL,
  translateBases = TRUE,
  genome = "hg38",
  phased = FALSE,
  region = NULL,
  sample = NULL
)

`vcfFile`	A path to a VCF file to be loaded.
`genoField`	A vector of genotype IDs to be loaded from VCF [e.g. 'GT']
`translateBases`	Set to `TRUE` if REF and ALT alleles should be reported as A,C,G or T.
`genome`	A reference genome used by readVcfAsVRanges function. [e.g. 'hg38' - human]
`phased`	If set to `TRUE` all unphased variants are removed.
`region`	A `GRanges` object of genomic regions to be loaded from input VCF file.
`sample`	A user defined set of sample IDs to be loaded.