run.vardict.sample: run.vardict.sample

Description

Run VarDict on a sample. Idea: have a low-level function that simply submits job to Perl, after BAM paths have been found. and output paths already have been decided upon

Usage

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

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.

proton

Logical indicating whether the data was generated by proton sequencing. Defaults to False (i.e. Illumina)

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

job.name

Name of job to be submitted

job.group

Group job should belong to

quiet

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

verify.options

Logical indicating whether to run verify.varitas.options