Entering edit mode
Stephanie M. Gogarten
▴
870
@stephanie-m-gogarten-5121
Last seen 5 months ago
University of Washington
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