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