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
>
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