verify.varitas.options: Check against common errors in the VariTAS options.

In varitas: Variant Calling in Targeted Analysis Sequencing Data

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

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