post.processing: Post-processing of variants to generate outputs

In varitas: Variant Calling in Targeted Analysis Sequencing Data

Description

Post-processing of variants to generate outputs

Usage

post.processing(variant.specification, project.directory,
  config.file = NULL, variant.callers = NULL,
  remove.structural.variants = TRUE,
  separate.consensus.filters = FALSE, sleep = FALSE, verbose = FALSE)

Arguments

variant.specification	Data frame specifying variants to be processed, or path to data frame (useful if calling from Perl)
project.directory	Directory where output should be stored. Output files will be saved to a datestamped subdirectory
config.file	Path to config file specifying post-processing options. If not provided, the current options are used (i.e. from get.varitas.options())
variant.callers	Optional vector of variant callers for which filters should be included in Excel file
remove.structural.variants	Logical indicating whether structural variants (including CNVs) should be removed. Defaults to TRUE.
separate.consensus.filters	Logical indicating whether to apply different thresholds to variants called by more than one caller (specified under consensus in config file). Defaults to FALSE.
sleep	Logical indicating whether script should sleep for 60 seconds before starting.
verbose	Logical indicating whether to print verbose output

Value

None

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