run.filtering.txt {varitas}

Run filtering on an ANNOVAR-annotated txt file

Description

Run filtering on an ANNOVAR-annotated txt file

Usage

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)

Arguments

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.