R: Filter VCF MuTect

filterVcfMuTect {PureCN}

R Documentation

Filter VCF MuTect

Description

Function to remove artifacts and low confidence/quality calls from a MuTect generated VCF file. Also applies filters defined in filterVcfBasic. This function will only keep variants listed in the stats file and those not matching the specified failure reasons.

Usage

filterVcfMuTect(vcf, tumor.id.in.vcf = NULL, stats.file = NULL,
  ignore = c("clustered_read_position", "fstar_tumor_lod",
  "nearby_gap_events", "poor_mapping_region_alternate_allele_mapq",
  "poor_mapping_region_mapq0", "possible_contamination", "strand_artifact",
  "seen_in_panel_of_normals"), ...)

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.
`stats.file`	MuTect stats file. If `NULL`, will check if VCF was generated by MuTect2 and if yes will call `filterVcfMuTect2` instead.
`ignore`	MuTect 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.vcf.gz", package="PureCN")
vcf <- readVcf(vcf.file, "hg19")
vcf.filtered <- filterVcfMuTect(vcf)

[Package PureCN version 1.10.0 Index]