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
