Stephanie M. Gogarten | 11 Jan 23:22 2013

merging VCF files

Hi all,

Does VariantAnnotation currently have a method to merge VCF objects? 
I've been looking through the documentation and code and haven't found 
anything like this.  If not, I think it would be a useful feature to add.

My use case: I have two VCF files, with the same samples (but in 
different order in each file).  The two files have non-overlapping 
variants.  I would love to have an rbind(VCF, VCF) method; then I could 
do something like:

vcf2 <- vcf2[,colnames(vcf1)]
vcf <- rbind(vcf1, vcf2)

cbind() would also be useful, for combining files with the same variants 
but different samples.

thanks,
Stephanie

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