varitas (version 0.0.2)

run.mutect.sample: Run MuTect for a sample

Description

Run MuTect for a sample

Usage

run.mutect.sample(tumour.bam, sample.id, paired, normal.bam = NULL,
  output.directory = NULL, output.filename = NULL,
  code.directory = NULL, log.directory = NULL, config.file = NULL,
  job.dependencies = NULL, quiet = FALSE, job.name = NULL,
  verify.options = !quiet, job.group = NULL)

Arguments

tumour.bam

Path to tumour sample BAM file.

sample.id

Sample ID for labelling

paired

Logical indicating whether to do variant calling with a matched normal.

normal.bam

Path to normal BAM file if paired = TRUE

output.directory

Path to output directory

output.filename

Name of resulting VCF file (defaults to SAMPLE_ID.vcf)

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

quiet

Logical indicating whether to print command to screen rather than submit it to the system. Defaults to false, useful for debugging.

job.name

Name of job to be submitted

verify.options

Logical indicating whether to run verify.varitas.options

job.group

Group job should belong to