post.processing {varitas}

Post-processing of variants to generate outputs

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