run.varitas.pipeline.hybrid {varitas}

run.varitas.pipeline.hybrid

Description

Run VariTAS pipeline starting from both VCF files and BAM/ FASTQ files. Useful for processing data from the Ion PGM or MiniSeq where variant calling has been done on the machine, but you are interested in running more variant callers.

Usage

run.varitas.pipeline.hybrid(vcf.specification, output.directory,
  run.name = NULL, fastq.specification = NULL,
  bam.specification = NULL, variant.callers = c("mutect", "vardict",
  "varscan", "lofreq", "muse"), proton = FALSE, quiet = FALSE,
  email = NULL, verify.options = !quiet,
  save.specification.files = !quiet)

Arguments

vcf.specification

Data frame containing details of vcf files to be processed. Must contain columns sample.id, vcf, and caller

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.

fastq.specification

Data frame containing details of FASTQ files to be processed

bam.specification

Data frame containing details of BAM files to be processed

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.hybrid(
       bam.specification = data.frame(sample.id = c('Z', 'Y'), tumour.bam = c('Z.bam', 'Y.bam')),
       vcf.specification = data.frame(
         sample.id = c('a', 'b'),
         vcf = c('a.vcf', 'b.vcf'),
         caller = c('pgm', 'pgm')
       ),
       output.directory = '.',
       quiet = TRUE,
       run.name = "Test", 
       variant.callers = c('mutect', 'varscan')
     )