run.varitas.pipeline.hybrid: run.varitas.pipeline.hybrid

In varitas: Variant Calling in Targeted Analysis Sequencing Data

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')
     )

varitas documentation built on Nov. 14, 2020, 1:07 a.m.