On Wed, Mar 19, 2014 at 4:00 PM, Michael Lawrence <lawrence.michael@gene.com
> wrote:

> It would be nice to have functions like isSNV, isIndel, isDeletion, etc
> that at least provide precise definitions of the terminology. I've added
> these, but they're designed only for VRanges. Should work for ExpandedVCF.
>
> Also, it would be nice if restrictToSNV just assumed that alt(x) must be
> something with nchar() support (with special handling for any List), so
> that the 'character' vector of alt,VRanges would work immediately.
> Basically restrictToSNV should just be x[isSNV(x)]. Is there even a
> use-case for the restrictToSNV abstraction if we did that?
>
>
for VCF instance it would be x[isSNV(x),] and indeed I think that would be
sufficient.  i like the idea of having this family of predicates for
variant classes to allow such selections



> Michael
>
>
>
> On Tue, Mar 18, 2014 at 10:36 AM, Valerie Obenchain <vobencha@fhcrc.org>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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>>
>
>

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