run.target.qc {varitas}

Perform sample QC by looking at target coverage.

Description

Perform sample QC by looking at target coverage.

Usage

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")

Arguments

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