Run a locally installed Ensembl VEP script on a VCF object or file

Calls a locally installed vep executable, annotates variants, and returns the result as a CollapsedVCF object. This complements vep_by_region, which uses the Ensembl REST API but is limited to 200 variants per request. The local script has no such limit and supports fully offline operation.

Usage

run_vep(x, assembly = "GRCh38", species = "homo_sapiens",
        fork = 1L, extra_args = character(), vep_path = NULL)

Arguments

x: A VCF object or character(1) path to a VCF file.
assembly: character(1) genome assembly passed to VEP via --assembly, e.g. "GRCh38" or "GRCh37".
species: character(1) species name as used by VEP, e.g. "homo_sapiens".
fork: integer(1) number of forks for parallel processing. Default 1L disables forking.
extra_args: character() additional flags passed verbatim to vep, e.g. c("--sift", "b", "--polyphen", "b") or "--offline".
vep_path: character(1) or NULL. Full path to the vep executable. When NULL (default) Sys.which("vep") is used.

Details

Requires a locally installed Ensembl VEP and a matching annotation cache. See https://www.ensembl.org/info/docs/tools/vep/script/vep_download.html for installation and cache setup instructions.

VEP is invoked with --vcf --no_stats --force_overwrite. The annotated output VCF is read back with readVcf and returned. Consequence annotations are stored in the CSQ field of info().

Pass "--offline" in extra_args for fully offline operation (requires a local cache).

Value

A CollapsedVCF object. VEP consequence annotations appear in info(result)$CSQ.

Examples

if (FALSE) { # \dontrun{
  fl <- system.file("extdata", "chr22.vcf.gz", package = "VariantAnnotation")
  vcf <- readVcf(fl)
  result <- run_vep(vcf[1:10], assembly = "GRCh38")
  info(result)$CSQ
} # }