verify.varitas.options {varitas}

Check against common errors in the VariTAS options.

Description

Check against common errors in the VariTAS options before launching into pipeline

Usage

verify.varitas.options(stages.to.run = c("alignment", "qc", "calling",
  "annotation", "merging"), variant.callers = c("mutect", "vardict",
  "ides", "varscan", "lofreq", "muse"), varitas.options = NULL)

Arguments

stages.to.run

Vector indicating which stages should be run. Defaults to all possible stages. If only running a subset of stages, only checks corresponding to the desired stages are run

variant.callers

Vector indicating which variant callers to run. Only used if calling is in stages.to.run.

varitas.options

Optional file path or list of VariTAS options.

Value

None