R function to run vcfanno

vcfanno(vcfanno = Sys.which(c("vcfanno", "vcfanno_osx", "vcfanno_linux64")),
  vcfanno.database.cfg = system.file("extdata", "demo/vcfanno_demo/conf.toml",
  package = "annovarR"), 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 annovarR 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)
#> vcfanno_linux64 -p 2 /Volumes/JianfengDisk/Backup/repositories/ljf/github/annovarR/inst/extdata/demo/vcfanno_demo/conf.toml input.vcf > output.vcf
#> [1] "vcfanno_linux64 -p 2 /Volumes/JianfengDisk/Backup/repositories/ljf/github/annovarR/inst/extdata/demo/vcfanno_demo/conf.toml input.vcf > output.vcf"