[BioC] Strand information for dbSNP packages

[Valerie Obenchain]

Thanks Herve. I think that explains it.

Valerie

On 02/28/12 17:35, Hervé Pagès wrote:
> Hi Alex,
>
> On 02/28/2012 03:50 PM, Valerie Obenchain wrote:
>> Hi Alex,
>>
>> On 02/28/2012 03:03 AM, Alex Gutteridge wrote:
>>> I notice the GRanges returned by the dbSNP packages have strand '*'.
>>> Does anyone know how safe am I in assuming that the variant alleles
>>> also given by the package actually correspond to the '+' strand?
>
> Yes the alleles actually always correspond to the + strand. I should
> clarify this in the man page. dbSNP reports the strand and alleles for
> a given SNP and the alleles they give is relative to the reported
> strand. However, when the SNPlocs.Hsapiens.dbSNP.20110815 package is
> made the alleles for SNPs on the minus strand are complemented so
> they correspond to the '+' strand. So all SNPs are considered to be
> on the + strand and everything is reported with respect to that strand.
>
> Hope this helps and sorry for the confusion.
>
> Cheers,
> H.
>
>>
>> The dbSNP packages don't contain any strand information so it isn't safe
>> to assume one strand or the other.
>>>
>>> I ask this in the context of trying to use predictCoding in the
>>> VariantAnnotations package to find coding SNPs. For SNPs in genes on
>>> the '-' strand I have found that I have to complement the alleles
>>> given by dbSNP to get the correct result. I just want to make sure
>>> that assuming the alleles are from the '+' strand is a reasonable
>>> assumption in the vast majority (>99%) of cases.
>>
>> This does not seem right, I'll look into it.
>>
>> Valerie
>>>
>>> I realise from my reading of the SNPlocs.Hsapiens.dbSNP.20110815
>>> manual that some SNPs will be incorrect anyway (it mentions ~0.1% of
>>> SNPs not mapping to the reference at all), that level of failure is
>>> acceptable, but anything higher would be a worry.
>>>
>>
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>
>