R: Filter VCF MuTect2

filterVcfMuTect2 {PureCN}

R Documentation

Filter VCF MuTect2

Description

Function to remove artifacts and low confidence/quality calls from a GATK4/MuTect2 generated VCF file. Also applies filters defined in filterVcfBasic.

Usage

filterVcfMuTect2(vcf, tumor.id.in.vcf = NULL, ignore = c("clustered_events",
  "t_lod", "str_contraction", "read_position", "fragment_length",
  "multiallelic", "clipping", "strand_artifact"), ...)

Arguments

`vcf`	`CollapsedVCF` object, read in with the `readVcf` function from the VariantAnnotation package.
`tumor.id.in.vcf`	The tumor id in the VCF file, optional.
`ignore`	MuTect2 flags that mark variants for exclusion.
`...`	Additional arguments passed to `filterVcfBasic`.

Value

A list with elements vcf, flag and flag_comment. vcf contains the filtered CollapsedVCF, flag a logical(1) flag if problems were identified, further described in flag_comment.

Author(s)

Markus Riester

Examples


### This function is typically only called by runAbsolute via the 
### fun.filterVcf and args.filterVcf comments.
library(VariantAnnotation)    
vcf.file <- system.file("extdata", "example.vcf.gz", package="PureCN")
vcf <- readVcf(vcf.file, "hg19")
vcf.filtered <- filterVcfMuTect(vcf)

[Package PureCN version 1.12.2 Index]