FilterVCF: FilterVCF

In cgab-ncc/FIREVAT: FIREVAT, FInding REliable Variants without ArTifacts

FilterVCF

Description

Filter vcf based on the filter Filtering parameters are saved in config.obj Split vcf.obj into vcf.obj.filtered & vcf.obj.artifact based on vcf.filter

Usage

FilterVCF(
  vcf.obj,
  vcf.filter,
  config.obj,
  include.array = NULL,
  force.include = FALSE,
  verbose = TRUE
)

Arguments

vcf.obj	A list from ReadVCF
vcf.filter	A list from MakeMuTect2Filter
config.obj	A list from ParseConfigFile
include.array	A boolean vector
force.include	A boolean value. If TRUE, then uses 'include.array'
verbose	If true, provides process detail

Value

A list with the following elements

• 1) Mutations which passed filteringvcf.obj.filtered = vcf.obj (list with data, header, genome)

• 2) Mutations which did not pass filteringvcf.obj.artifact = vcf.obj (list with data, header, genome)

cgab-ncc/FIREVAT documentation built on Nov. 19, 2022, 5:55 p.m.