[Bioc-devel] restrictToSNV for VCF

Valerie Obenchain vobencha at fhcrc.org
Tue Mar 18 18:36:45 CET 2014


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


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