[BioC] Querying dbSNP

[Steffen at stat.Berkeley.EDU]

Also to note is that biomaRt indeed queries Ensembl for SNP queries and
these SNPs are from dbSNP mapped to Ensembl.

The latest release notes from Ensembl 56 state:

Ensembl variation mart 56

    * Removal of Ensembl Celera, TSC and HGVBase information
    * Human now on dbSNP 130


Cheers,
Steffen

> It may also be noteworthy that the SNPlocs.Hsapiens.dbSNP.20090506
> package has location and allele information for build 130 dbSNP
> entries. A substantial quantity of SNP-related metadata is present in
> the pd.genomewidesnp.6 annotation package.
>
>  'Queries' to dbSNP of a more general nature could probably be
> programmed using various web services support packages in R/bioc.  If
> you describe a compelling use case, code might be written to solve it.
>
> On Mon, Oct 19, 2009 at 4:30 PM, Marc Carlson <mcarlson at fhcrc.org> wrote:
>> Hi Sharon,
>>
>> It's not clear to me from your email what you intend to do, but I know
>> that some dbSNP data is available as a UCSC track and should therefore
>> be obtainable by using the rtracklayer package.
>>
>>  Marc
>>
>>
>> Sharon wrote:
>>> Dear All,
>>>
>>> Is there any tool in Bioconductor to query dbSNP? I know that (correct
>>> me,
>>> if I am wrong) biomaRt is primarily for Ensemble.
>>>
>>> Thanks in advance.
>>>
>>> Kind regards,
>>> Sharon.
>>>
>>>       [[alternative HTML version deleted]]
>>>
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>>
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>
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