run.annotation {varitas}

Run annotation on a set of VCF files

Description

Takes a data frame with paths to VCF files, and runs ANNOVAR annotation on each file. To allow for smooth connections with downstream pipeline steps, the function returns a variant specification data frame that can be used as input to merging steps.

Usage

run.annotation(vcf.specification, output.directory = NULL,
  job.name.prefix = NULL, job.group = NULL, quiet = FALSE,
  verify.options = !quiet)

Arguments

vcf.specification

Data frame detailing VCF files to be processed, from prepare.vcf.specification.

output.directory

Path to folder where code and log files should be stored in their respective subdirectories. If not supplied, code and log files will be stored in the directory with each VCF file.

job.name.prefix

Prefix to be added before VCF name in job name. Defaults to 'annotate', but should be changed if running multiple callers to avoid

job.group

Group job should be associated with on cluster

quiet

Logical indicating whether to print commands to screen rather than submit them

verify.options

Logical indicating whether to run verify.varitas.options

Value

Data frame with details of variant files

Examples

run.annotation(
  data.frame(
    sample.id = c('a', 'b'),
    vcf = c('a.vcf', 'b.vcf'),
    caller = c('mutect', 'mutect')
  ),
  output.directory = '.',
  quiet = TRUE
)