run.target.qc: Perform sample QC by looking at target coverage.
In varitas: Variant Calling in Targeted Analysis Sequencing Data

Perform sample QC by looking at target coverage.

run.target.qc(bam.specification, project.directory,
  sample.directories = TRUE, paired = FALSE,
  output.subdirectory = FALSE, quiet = FALSE, job.name.prefix = NULL,
  verify.options = FALSE, job.group = "target_qc")

`bam.specification`	Data frame containing details of BAM files to be processed, typically from `prepare.bam.specification`.
`project.directory`	Path to project directory where code and log files should be saved
`sample.directories`	Logical indicating whether output for each sample should be put in its own directory (within output.directory)
`paired`	Logical indicating whether the analysis is paired. This does not affect QC directly, but means normal samples get nested
`output.subdirectory`	If further nesting is required, name of subdirectory. If no further nesting, set to FALSE
`quiet`	Logical indicating whether to print commands to screen rather than submit the job
`job.name.prefix`	Prefix for job names on the cluster
`verify.options`	Logical indicating whether to run verify.varitas.options
`job.group`	Group job should be associated with on cluster