[BioC] dbSNP build for R package SNPlocs.Hsapiens.dbSNP.20080617

[James W. MacDonald]

Hi Herve,

I've been dealing with these data myself recently, and can confirm that 
the data in March were build 129. They put the build 130 data up in 
early May.

As a side note, build 129 is known to be problematic, as there are 
multiple RS numbers that map to the same location:

http://www.ncbi.nlm.nih.gov/mailman/pipermail/dbsnp-announce/2008q2/000082.html

According to their help team, this problem has been resolved in build 130.

Best,

Jim



Hervé Pagès wrote:
> Hi Lin,
> 
> I'm cc'ing the BioC list so other users might benefit from this.
> 
> Lin Tang wrote:
>> Dear Dr. Pages,
>>
>>  
>>
>>
>>   I am using R package SNPlocs.Hsapiens.dbSNP.20080617 currently, I want
>>   to check with you that whether this package corresponds to dbSNP build
>>   129 ? Although from the release date of this R package which is two
>>   months after the release of dbSNP build 129, it is logical to be so. I
>>   want to have it confirmed from you. I’d appreciate your kind reply on
>>   this. Thanks!
> 
> It's hard to tell.
> 
> According to these pages:
>   
> http://www.ncbi.nlm.nih.gov/mailman/pipermail/dbsnp-announce/2008q2/000081.html 
> 
>   http://www.ncbi.nlm.nih.gov/projects/SNP/buildhistory.cgi
> Build 129 was released in April 2008 (note that the exact dates found on 
> these
> 2 pages don't match).
> 
> A similar research shows that Build 130 was released about 1 month ago.
> 
> So at the time I downloaded the ds_flat_ch*.flat files from here
>   ftp://ftp.ncbi.nih.gov/snp/organisms/human_9606/ASN1_flat
> in order to build SNPlocs.Hsapiens.dbSNP.20080617 (that was in March
> 2009), I assume that these files were a dump from Build 129.
> 
> Note that the files under
>   ftp://ftp.ncbi.nih.gov/snp/organisms/human_9606/ASN1_flat
> can change at anytime (and today they are indeed different from what they
> were back in March). It's a sad thing that the SNP team at NCBI doesn't
> provide permanent URLs for their past builds. And it doesn't help that
> the ds_flat_ch*.flat files they provide don't contain any information
> about the build that they're coming from.
> 
> Anyway, in the future I'll put the Build information in the DESCRIPTION
> file of the SNPlocs packages.
> 
> One last note. According to the SNP team at NCBI "Human SNPs in Build 129
> are mapping to NCBI build 36.3". That is, to our 
> BSgenome.Hsapiens.UCSC.hg18
> package. According to UCSC, hg18 is NCBI Build 36.1 but NCBI Build 36.1 and
> NCBI Build 36.3 are identical from a *sequence* point of view (I think what
> makes them different are the annotations provided by NCBI).
> This means that, if you are planning to inject 
> SNPlocs.Hsapiens.dbSNP.20080617
> in a genome, it only makes sense to do it with BSgenome.Hsapiens.UCSC.hg18.
> 
> In the future we will put in place a mechanism to make this injection safer
> i.e. check that the injected stuff and the host are compatible.
> 
> Cheers,
> H.
> 
> 
>>
>>
>>   Regards,
>>
>> Lin Tang, Ph.D.
>>
>> Scientist , Informatics | Sequenom  Inc.
>>
>> T: 1 858 202 9106 | F: 1 858 202 9084 | E: ltang at sequenom.com
>>
>>  
>>
>>
>>
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> 

-- 
James W. MacDonald, M.S.
Biostatistician
Douglas Lab
University of Michigan
Department of Human Genetics
5912 Buhl
1241 E. Catherine St.
Ann Arbor MI 48109-5618
734-615-7826