filterVcfMuTect: Filter VCF MuTect

In lima1/PureCN: Copy number calling and SNV classification using targeted short read sequencing

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

See Also

filterVcfBasic

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)        

lima1/PureCN documentation built on Sept. 17, 2024, 5:48 a.m.