run.target.qc.sample: Get ontarget reads and run coverage quality control
In varitas: Variant Calling in Targeted Analysis Sequencing Data

Get ontarget reads and run coverage quality control

run.target.qc.sample(bam.file, sample.id, output.directory = NULL,
  code.directory = NULL, log.directory = NULL, config.file = NULL,
  job.dependencies = NULL, job.name = NULL, job.group = NULL,
  quiet = FALSE)

`bam.file`	Path to BAM file
`sample.id`	Sample ID for labelling
`output.directory`	Path to output directory
`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.name`	Name of job to be submitted
`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.