R/vcftools.r

In bioDS/phyloRNA: Tools for phylogenetic analyses of scRNAseq data

#' Filter VCF file
#'
#' Filter a VCF file using the external `vcftools` software, removing indels and keeping
#' keeping only those SNVs that passed all filters.
#'
#' @param input an input VCF file
#' @param output an output VCF file
#' @template remake
#' @export
vcftools_filter = function(input, output, remake=FALSE){
    if(!remake && file.exists(output))
        return(invisible())

    readcmd = "--vcf"
    writecmd = "--stdout"

    if(tools::file_ext(input) == "gz")
        readcmd = "--gzvcf"

    if(tools::file_ext(output) == "gz")
        writecmd = c(writecmd, "|", getOption("phyloRNA.gzip"), "-c")

    args = c(
        readcmd, input,
        "--remove-filtered-all",
        "--remove-indels",
        "--recode",
        writecmd, ">", output
        )

    command = getOption("phyloRNA.vcftools")
    systemE(command=command, args=args)
    }