run.target.qc.sample {varitas}

Get ontarget reads and run coverage quality control

Description

Get ontarget reads and run coverage quality control

Usage

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)

Arguments

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.