concat.vcf: Concatenates two vcf files tohether

In erickramer/batch.vcf: What the package does (short line)

Usage

concat.vcf(vcf1, vcf2, vcf3 = NULL, tmpdir = tempdir())

Arguments

vcf1
vcf2
vcf3
tmpdir

Examples

##---- Should be DIRECTLY executable !! ----
##-- ==>  Define data, use random,
##--	or do  help(data=index)  for the standard data sets.

## The function is currently defined as
function (vcf1, vcf2, vcf3 = NULL, tmpdir = tempdir()) 
{
    if (is.null(vcf1)) 
        return(vcf2)
    if (is.null(vcf2)) 
        return(vcf1)
    vcf3 = if (is.null(vcf3)) 
        temp.file(tmpdir = tmpdir)
    else vcf3
    system(paste("bcftools concat", "-o", vcf3, "-O z", vcf1, 
        vcf2))
    return(vcf3)
  }

erickramer/batch.vcf documentation built on May 16, 2019, 8:28 a.m.