run.variant.calling: run.variant.calling
In varitas: Variant Calling in Targeted Analysis Sequencing Data

Description Usage Arguments Details Value Examples

Run variant calling for all samples

run.variant.calling(bam.specification, output.directory,
  variant.callers = c("vardict", "mutect", "varscan", "lofreq", "muse"),
  paired = TRUE, proton = FALSE, sample.directories = TRUE,
  job.name.prefix = NULL, quiet = FALSE, verify.options = !quiet)

`bam.specification`	Data frame containing details of BAM files to be processed, typically from `prepare.bam.specification`.
`output.directory`	Path to directory where output should be saved
`variant.callers`	Character vector of variant callers to be used
`paired`	Logical indicating whether to do variant calling with a matched normal
`proton`	Logical indicating whether data was generated by proton sequencing (ignored if running MuTect)
`sample.directories`	Logical indicating whether output for each sample should be put in its own directory (within output.directory)
`job.name.prefix`	Prefix for job names on the cluster
`quiet`	Logical indicating whether to print commands to screen rather than submit the job
`verify.options`	Logical indicating whether to run verify.varitas.options

Run VarDict on each sample, and annotate the results with ANNOVAR. Files are output to a vardict/ subdirectory within each sample directory.

None

run.variant.calling(
  data.frame(sample.id = c('Z', 'Y'), tumour.bam = c('Z.bam', 'Y.bam')),
  output.directory = '.',
  variant.caller = c('lofreq', 'mutect'),
  quiet = TRUE,
  paired = FALSE
)