[BioC] merging VCF files

[Valerie Obenchain]

rbind and cbind are now implemented for SummarizedExperiment 
(GenomicRanges 1.11.29) and VCF (VariantAnnotation 1.5.34).

rbind is appropriate for the case of different ranges (variants) and the 
same samples. cbind is appropriate for the same ranges and different 
samples.

Let me know if you run into problems/bugs.

Valerie


On 01/11/2013 02:22 PM, Stephanie M. Gogarten wrote:
> 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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