vcfanno: R function to run vcfanno

In JhuangLab/annovarR: Integrated Framework to Annotate Genetic Variants

Description

R function to run vcfanno

Usage

vcfanno(
  vcfanno = Sys.which(c("vcfanno", "vcfanno_osx", "vcfanno_linux64")),
  vcfanno_database_cfg = system.file("extdata", "demo/vcfanno_demo/conf.toml", package
    = "anor"),
  base_path = "",
  lua = "",
  ends = FALSE,
  input.file = "input.vcf",
  out = "output.vcf",
  thread = 2,
  permissive_overlap = FALSE,
  debug = FALSE
)

Arguments

vcfanno	Executable file of vcfanno (Download from https://github.com/brentp/vcfanno/releases)
vcfanno_database_cfg	vcfanno required database configuration file (Not the anor database.cfg)
base_path	Optional base_path to prepend to annotation files in the config
lua	Optional path to a file containing custom javascript functions to be used as ops
ends	Annotate the start and end as well as the interval itself.
input.file	Input file path (VCF only)
out	Output file path
thread	number of processes to use. (default 2)
permissive_overlap	annotate with an overlapping variant even it doesn't share the same ref and alt alleles. Default is to require exact match between variants.
debug	If set TRUE, only print the command

Examples

vcfanno(debug = TRUE)

JhuangLab/annovarR documentation built on April 23, 2020, 10:51 p.m.