filter.variant.file: Filter variants in file.

In varitas: Variant Calling in Targeted Analysis Sequencing Data

Description

Filter variants from file, and save to output. Wrapper function that opens the variant file, calls filter.variants, and saves the result to file

Usage

filter.variant.file(variant.file, output.file, config.file = NULL,
  caller = c("vardict", "ides", "mutect", "pgm", "consensus"))

Arguments

variant.file	Path to variant file
output.file	Path to output file
config.file	Path to config file to be used. If not supplied, will use the pre-existing VariTAS options.
caller	Name of caller used (needed to match appropriate filters from settings)

Value

None

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