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

### 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]