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

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 > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor