[Bioc-devel] restrictToSNV for VCF

Stephanie M. Gogarten sdmorris at u.washington.edu
Wed Mar 19 19:42:31 CET 2014

I would say rows 1 and 3 are SNVs, but not row 4.  For this application 
I think a variant has to be an SNV or not, as you can't pass half a 
variant.  (I suppose you could remove the ALT values with length > 1 and 
set those genotypes to missing, but that is both complicated and 
unexpected behavior.  Also, it could introduce bias into association 
testing, since you would get non-random missingness.)

isSNV() in SeqVarTools returns TRUE only if the max length of all 
alleles is 1.  It also has a logical argument "biallelic" which allows 
to select for only biallelic SNVs - that could be useful here as well. 
If biallelic=TRUE, only row 1 would make it into the subset.


On 3/18/14 4:04 PM, Julian Gehring wrote:
> 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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