Description Usage Arguments Examples
View source: R/external_tools.R
R function to run vcfanno
1 2 3 4 5 | 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)
|
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 |
1 |
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