run.filtering.txt: Run filtering on an ANNOVAR-annotated txt file
In varitas: Variant Calling in Targeted Analysis Sequencing Data

Run filtering on an ANNOVAR-annotated txt file

run.filtering.txt(variant.file, caller = c("consensus", "vardict",
  "ides", "mutect"), output.directory = NULL, output.filename = NULL,
  code.directory = NULL, log.directory = NULL, config.file = NULL,
  job.dependencies = NULL, job.group = NULL, quiet = FALSE)

`variant.file`	Path to variant file
`caller`	String giving variant caller that was used (affects which filters were applied.
`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
`quiet`	Logical indicating whether to print command to screen rather than submit it to the system. Defaults to false, useful for debugging.