11 Jan 2013 23:22
merging VCF files
Stephanie M. Gogarten <sdmorris <at> u.washington.edu>
2013-01-11 22:22:02 GMT
2013-01-11 22:22:02 GMT
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@... https://stat.ethz.ch/mailman/listinfo/bioconductor Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
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