merge.variants {varitas}

Merge variants

Description

Merge variants from multiple callers and return a data frame of merged calls. By default filtering is also applied, although this behaviour can be turned off by setting apply.filters to FALSE.

Usage

## S3 method for class 'variants'
merge(variant.specification, apply.filters = TRUE,
  remove.structural.variants = TRUE,
  separate.consensus.filters = FALSE, verbose = FALSE)

Arguments

variant.specification

Data frame containing details of file paths, sample IDs, and caller.

apply.filters

Logical indicating whether to apply filters. Defaults to TRUE.

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.

verbose

Logical indicating whether to print information to screen

Value

Data frame