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

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".

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

Results

R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

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Type 'license()' or 'licence()' for distribution details.

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Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(PureCN)
Loading required package: DNAcopy
Loading required package: VariantAnnotation
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, cbind, colnames, do.call, duplicated, eval, evalq,
    get, grep, grepl, intersect, is.unsorted, lapply, lengths, mapply,
    match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank,
    rbind, rownames, sapply, setdiff, sort, table, tapply, union,
    unique, unsplit

Loading required package: GenomeInfoDb
Loading required package: stats4
Loading required package: S4Vectors

Attaching package: 'S4Vectors'

The following objects are masked from 'package:base':

    colMeans, colSums, expand.grid, rowMeans, rowSums

Loading required package: IRanges
Loading required package: GenomicRanges
Loading required package: SummarizedExperiment
Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: Rsamtools
Loading required package: Biostrings
Loading required package: XVector

Attaching package: 'VariantAnnotation'

The following object is masked from 'package:base':

    tabulate

> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/PureCN/filterVcfMuTect.Rd_%03d_medium.png", width=480, height=480)
> ### Name: filterVcfMuTect
> ### Title: Filter VCF MuTect
> ### Aliases: filterVcfMuTect
> 
> ### ** 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)        
Removing 0 non heterozygous (in matched normal) germline SNPs.
Removing 108 SNPs with AF < 0.03 or AF >= 0.97 or less than 3 supporting reads or depth < 20.
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>