run.lofreq.sample: Run LoFreq for a sample
In varitas: Variant Calling in Targeted Analysis Sequencing Data

Run LoFreq for a sample

run.lofreq.sample(tumour.bam, sample.id, paired, normal.bam = NULL,
  output.directory = NULL, output.filename = NULL,
  code.directory = NULL, log.directory = NULL, config.file = NULL,
  job.dependencies = NULL, quiet = FALSE, job.name = NULL,
  verify.options = !quiet, job.group = NULL)

`tumour.bam`	Path to tumour sample BAM file.
`sample.id`	Sample ID for labelling
`paired`	Logical indicating whether to do variant calling with a matched normal.
`normal.bam`	Path to normal BAM file if `paired = TRUE`
`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
`quiet`	Logical indicating whether to print command to screen rather than submit it to the system. Defaults to false, useful for debugging.
`job.name`	Name of job to be submitted
`verify.options`	Logical indicating whether to run verify.varitas.options
`job.group`	Group job should belong to