run.variant.calling {varitas}

run.variant.calling

Description

Run variant calling for all samples

Usage

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)

Arguments

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

Details

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

Value

None

Examples

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
)