varitas (version 0.0.2)

filter.variants: Filter variant calls

Description

Filter data frame of variant calls based on thresholds specified in settings.

Usage

filter.variants(variants, caller = c("vardict", "ides", "mutect", "pgm",
  "consensus", "isis", "varscan", "lofreq"), config.file = NULL,
  verbose = FALSE)

Arguments

variants

Data frame of variant calls with ANNOVAR annotation, or path to variant file.

caller

Name of caller used (needed to match appropriate filters from settings)

config.file

Path to config file to be used. If not supplied, will use the pre-existing VariTAS options.

verbose

Logical indicating whether to output descriptions of filtering steps. Defaults to False, useful for debugging.

Value

filtered.variants Data frame of filtered variants