run.alignment: Run alignment
In varitas: Variant Calling in Targeted Analysis Sequencing Data

Description Usage Arguments Details Value Examples

Run alignment

run.alignment(fastq.specification, output.directory, paired.end = FALSE,
  sample.directories = TRUE, output.subdirectory = FALSE,
  job.name.prefix = NULL, job.group = "alignment", quiet = FALSE,
  verify.options = !quiet)

`fastq.specification`	Data frame detailing FASTQ files to be processed, typically from prepare.fastq.specification
`output.directory`	Path to project directory
`paired.end`	Logical indicating whether paired-end sequencing was performed
`sample.directories`	Logical indicating whether all sample files should be saved to sample-specific subdirectories (will be created)
`output.subdirectory`	If further nesting is required, name of subdirectory. If no further nesting, set to FALSE
`job.name.prefix`	Prefix for job names on the cluster
`job.group`	Group job should be associated with on cluster
`quiet`	Logical indicating whether to print commands to screen rather than submit them
`verify.options`	Logical indicating whether to run verify.varitas.options

Runs alignment (and related processing steps) on each sample.

None

run.alignment(
  fastq.specification = data.frame(
    sample.id = c('1', '2'),
    reads = c('1-R1.fastq.gz', '2-R1.fastq.gz'),
    mates = c('1-R2.fastq.gz', '2-R2.fastq.gz'),
    patient.id = c('P1', 'P1'),
    tissue = c('tumour', 'normal')
  ),
  output.directory = '.',
  quiet = TRUE,
  paired.end = TRUE
)