[BioC] merging VCF files

[Valerie Obenchain]

Good suggestion. I'll implement something in the next couple of weeks.

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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