PureCN (version 1.0.3)

filterVcfMuTect: Filter VCF MuTect

Description

Function to remove artifacts and low confidence/quality calls from a MuTect generated VCF file.

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"), verbose = TRUE, ...)

Arguments

vcf

VCF 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

ignore

verbose

Verbose output.

...

Additional arguments passed to filterVcfBasic

Value

• A list with elements vcf, flag and flag_comment. "vcf" contains the filtered CollapsedVCF, "flag" a flag if problems were identified, further described in "flag_comment".

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", package="PureCN")
vcf <- readVcf(vcf.file, "hg19")
vcf.filtered <- filterVcfMuTect(vcf)