Hi Valerie, I would consider G>C an SNV, G>TT not. But I assume that there exists no clear consensus on this. How about a flag that let's the second pass as SNV optionally, so everybody can get what one needs?
Best wishes Julian On 18/03/14 18:36, Valerie Obenchain wrote: > Hi, > > I've added a restrictToSNV() function to VariantAnnotation (1.9.46). The > return value is a subset VCF object containing SNVs only. The function > operates on CollapsedVCF or ExapandedVCF and the alt(VCF) value must be > nucleotides (i.e., no structural variants). > > A variant is considered a SNV if the nucleotide sequences in both > ref(vcf) and alt(x) are of length 1. I have a question about how > variants with multiple 'ALT' values should be handled. > > Should we consider row 4 a SNV? One 'ALT' is length 1, the other is not. > > ALT <- DNAStringSetList("A", c("TT"), c("G", "A"), c("TT", "C")) > REF <- DNAStringSet(c("G", c("AA"), "T", "G")) >>> DataFrame(REF, ALT) >> DataFrame with 4 rows and 2 columns >> REF ALT >> <DNAStringSet> <DNAStringSetList> >> 1 G A >> 2 AA TT >> 3 T G,A >> 4 G TT,C > > > Thanks. > Valerie > > _______________________________________________ > Bioc-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/bioc-devel _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel