filterVars {systemPipeR} | R Documentation

## Filter VCF files

### Description

Convenience function for filtering VCF files based on user definable quality parameters. The function imports each VCF file into R, applies the filtering on an internally generated `VRanges` object and then writes the results to a new VCF file.

### Usage

    filterVars(args, filter, varcaller, organism)

### Arguments

`args` | Object of class `SYSargs`. The paths of the input VCF files are specified under `infile1(args)` and the paths of the output files under `outfile1(args)`.
`filter` | Character vector of length one specifying the filter syntax that will be applied to the internally created `VRanges` object.
`varcaller` | Character vector of length one specifying the variant caller used for generating the input VCFs. Currently, this argument can be assigned 'gatk', 'bcftools' or 'vartools'.
`organism` | Character vector specifying the organism name of the reference genome.

### Value

Output files in VCF format. Their paths can be obtained with `outpaths(args)`.

### Author(s)

Thomas Girke

### See Also

`variantReport` `combineVarReports`, `varSummar`

### Examples

    ## Alignment with BWA (sequentially on single machine)
    param <- system.file("extdata", "bwa.param", package="systemPipeR")
    targets <- system.file("extdata", "targets.txt", package="systemPipeR")
    args <- systemArgs(sysma=param, mytargets=targets)
    sysargs(args)[1]

    ## Not run:
    system("bwa index -a bwtsw ./data/tair10.fasta")
    bampaths <- runCommandline(args=args)

    ## Alignment with BWA (parallelized on compute cluster)
    resources <- list(walltime="20:00:00", nodes=paste0("1:ppn=", cores(args)), memory="10gb")
    reg <- clusterRun(args, conffile=".BatchJobs.R", template="torque.tmpl", Njobs=18, runid="01",
                      resourceList=resources)

    ## Variant calling with GATK
    ## The following creates in the inital step a new targets file
    ## (targets_bam.txt). The first column of this file gives the paths to
    ## the BAM files created in the alignment step. The new targets file and the
    ## parameter file gatk.param are used to create a new SYSargs
    ## instance for running GATK. Since GATK involves many processing steps, it is
    ## executed by a bash script gatk_run.sh where the user can specify the
    ## detailed run parameters. All three files are expected to be located in the
    ## current working directory. Samples files for gatk.param and
    ## gatk_run.sh are available in the subdirectory ./inst/extdata/ of the
    ## source file of the systemPipeR package.
    writeTargetsout(x=args, file="targets_bam.txt")
    system("java -jar CreateSequenceDictionary.jar R=./data/tair10.fasta O=./data/tair10.dict")
    # system("java -jar /opt/picard/1.81/CreateSequenceDictionary.jar R=./data/tair10.fasta O=./data/tair10.dict")
    args <- systemArgs(sysma="gatk.param", mytargets="targets_bam.txt")
    resources <- list(walltime="20:00:00", nodes=paste0("1:ppn=", 1), memory="10gb")
    reg <- clusterRun(args, conffile=".BatchJobs.R", template="torque.tmpl", Njobs=18, runid="01",
                      resourceList=resources)
    writeTargetsout(x=args, file="targets_gatk.txt")

    ## Variant calling with BCFtools
    ## The following runs the variant calling with BCFtools. This step requires in
    ## the current working directory the parameter file sambcf.param and the
    ## bash script sambcf_run.sh.
    args <- systemArgs(sysma="sambcf.param", mytargets="targets_bam.txt")
    resources <- list(walltime="20:00:00", nodes=paste0("1:ppn=", 1), memory="10gb")
    reg <- clusterRun(args, conffile=".BatchJobs.R", template="torque.tmpl", Njobs=18, runid="01",
                      resourceList=resources)
    writeTargetsout(x=args, file="targets_sambcf.txt")

    ## Filtering of VCF files generated by GATK
    args <- systemArgs(sysma="filter_gatk.param", mytargets="targets_gatk.txt")
    filter <- "totalDepth(vr) >= 2 & (altDepth(vr) / totalDepth(vr) >= 0.8) & rowSums(softFilterMatrix(vr))==4"
    # filter <- "totalDepth(vr) >= 20 & (altDepth(vr) / totalDepth(vr) >= 0.8) & rowSums(softFilterMatrix(vr))==6"
    filterVars(args, filter, varcaller="gatk", organism="A. thaliana")
    writeTargetsout(x=args, file="targets_gatk_filtered.txt")

    ## Filtering of VCF files generated by BCFtools
    args <- systemArgs(sysma="filter_sambcf.param", mytargets="targets_sambcf.txt")
    filter <- "rowSums(vr) >= 2 & (rowSums(vr[,3:4])/rowSums(vr[,1:4]) >= 0.8)"
    # filter <- "rowSums(vr) >= 20 & (rowSums(vr[,3:4])/rowSums(vr[,1:4]) >= 0.8)"
    filterVars(args, filter, varcaller="bcftools", organism="A. thaliana")
    writeTargetsout(x=args, file="targets_sambcf_filtered.txt")

    ## Annotate filtered variants from GATK
    args <- systemArgs(sysma="annotate_vars.param", mytargets="targets_gatk_filtered.txt")
    txdb <- loadDb("./data/tair10.sqlite")
    fa <- FaFile(systemPipeR::reference(args))
    variantReport(args=args, txdb=txdb, fa=fa, organism="A. thaliana")

    ## Annotate filtered variants from BCFtools
    args <- systemArgs(sysma="annotate_vars.param", mytargets="targets_sambcf_filtered.txt")
    txdb <- loadDb("./data/tair10.sqlite")
    fa <- FaFile(systemPipeR::reference(args))
    variantReport(args=args, txdb=txdb, fa=fa, organism="A. thaliana")

    ## Combine results from GATK
    args <- systemArgs(sysma="annotate_vars.param", mytargets="targets_gatk_filtered.txt")
    combineDF <- combineVarReports(args, filtercol=c(Consequence="nonsynonymous"))
    write.table(combineDF, "./results/combineDF_nonsyn_gatk.xls", quote=FALSE, row.names=FALSE, sep="\t")

    ## Combine results from BCFtools
    args <- systemArgs(sysma="annotate_vars.param", mytargets="targets_sambcf_filtered.txt")
    combineDF <- combineVarReports(args, filtercol=c(Consequence="nonsynonymous"))
    write.table(combineDF, "./results/combineDF_nonsyn_sambcf.xls", quote=FALSE, row.names=FALSE, sep="\t")

    ## Summary for GATK
    args <- systemArgs(sysma="annotate_vars.param", mytargets="targets_gatk_filtered.txt")
    write.table(varSummary(args), "./results/variantStats_gatk.xls", quote=FALSE, col.names = NA, sep="\t")

    ## Summary for BCFtools
    args <- systemArgs(sysma="annotate_vars.param", mytargets="targets_sambcf_filtered.txt")
    write.table(varSummary(args), "./results/variantStats_sambcf.xls", quote=FALSE, col.names = NA, sep="\t")

    ## Venn diagram of variants
    args <- systemArgs(sysma="annotate_vars.param", mytargets="targets_gatk_filtered.txt")
    varlist <- sapply(names(outpaths(args))[1:4], function(x) as.character(read.delim(outpaths(args)[x])$VARID))
    vennset_gatk <- overLapper(varlist, type="vennsets")
    args <- systemArgs(sysma="annotate_vars.param", mytargets="targets_sambcf_filtered.txt")
    varlist <- sapply(names(outpaths(args))[1:4], function(x) as.character(read.delim(outpaths(args)[x])$VARID))
    vennset_bcf <- overLapper(varlist, type="vennsets")
    vennPlot(list(vennset_gatk, vennset_bcf), mymain="", mysub="GATK: red; BCFtools: blue", colmode=2, ccol=c("blue", "red"))

    ## End(Not run)

[Package systemPipeR version 1.18.2 Index]