Read a VCF file

Parse a Variant Call Format (VCF 4.x) file and return a tidy tibble of variant calls.

Usage

mp_read_vcf(path)

Arguments

path

Character scalar. Path to a .vcf or .vcf.gz file.

Value

A molpath_parsed object whose data slot is a tibble with columns chrom, pos, id, ref, alt, qual, filter, info, and any sample-level columns present in the file.

Details

The function first attempts to use VariantAnnotation::readVcf() from Bioconductor. If the package is not installed it falls back to a lightweight text parser that handles single- and multi-sample VCFs.

Examples

# \donttest{
vcf_file <- system.file("extdata", "example.vcf", package = "molpathR")
if (nzchar(vcf_file)) {
  result <- mp_read_vcf(vcf_file)
  print(result)
}
# }