run.varitas.pipeline {varitas}

Run VariTAS pipeline in full.

Description

Run all steps in VariTAS processing pipeline, with appropriate dependencies.

Usage

run.varitas.pipeline(file.details, output.directory, run.name = NULL,
  start.stage = c("alignment", "qc", "calling", "annotation", "merging"),
  variant.callers = NULL, proton = FALSE, quiet = FALSE,
  email = NULL, verify.options = !quiet,
  save.specification.files = !quiet)

Arguments

file.details

Data frame containing details of files to be used during first processing step. Depending on what you want to be the first step in the pipeline, this can either be FASTQ files, BAM files, VCF files, or variant (txt) files.

output.directory

Main directory where all files should be saved

run.name

Name of pipeline run. Will be added as a prefix to all LSF jobs.

start.stage

String indicating which stage pipeline should start at. If starting at a later stage of the pipeline, appropriate input files must be provided. For example, if starting with annotation, VCF files with variant calls must be provided.

variant.callers

Vector specifying which variant callers should be run.

proton

Logical indicating if data was generated by proton sequencing. Used to set base quality thresholds in variant calling steps.

quiet

Logical indicating whether to print commands to screen rather than submit jobs. Defaults to FALSE, can be useful to set to TRUE for testing.

email

Email address that should be notified when pipeline finishes. If NULL or FALSE, no email is sent.

verify.options

Logical indicating whether to run verify.varitas.options

save.specification.files

Logical indicating if specification files should be saved to project directory

Value

None

Examples

run.varitas.pipeline(
       file.details = 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,
       run.name = "Test", 
       variant.callers = c('mutect', 'varscan')
     )