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

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

[Package PureCN version 1.10.0 Index]