varitas (version 0.0.2)

run.annovar.vcf: Run ANNOVAR on a VCF file

Description

Run ANNOVAR on a VCF file

Usage

run.annovar.vcf(vcf.file, output.directory = NULL,
  output.filename = NULL, code.directory = NULL,
  log.directory = NULL, config.file = NULL, job.dependencies = NULL,
  job.group = NULL, job.name = NULL, isis = FALSE, quiet = FALSE,
  verify.options = !quiet)

Arguments

vcf.file

Path to VCF file

output.directory

Path to output directory

output.filename

Name of resulting VCF file (defaults to SAMPLE_ID.vcf)

code.directory

Path to directory where code should be stored

log.directory

Path to directory where log files should be stored

config.file

Path to config file

job.dependencies

Vector with names of job dependencies

job.group

Group job should belong to

job.name

Name of job to be submitted

isis

Logical indicating whether VCF files are from the isis (MiniSeq) variant caller

quiet

Logical indicating whether to print command to screen rather than submit it to the system. Defaults to false, useful for debugging.

verify.options

Logical indicating whether to run verify.varitas.options

Value

None