[ensembl-dev] incorporation of dbSNP 132 into ensembl

Pontus Larsson Pontus.Larsson at ebi.ac.uk
Thu Dec 9 14:41:34 GMT 2010


Hi Andrea,

Adding to Fiona's answer, the dbSNP 132 release for cow was slightly 
delayed so we were unable to import it in time for the January Ensembl 
release (61). This will instead happen for release 62.

If a variation has no mapping to the genome, you won't get any variation 
features at all.

/Pontus


On 09/12/2010 14:27, Andrea Edwards wrote:
>
> Dear all
>
>
> I was hoping you might be able to help me with something to do with 
> the incorporation of dbSNP 132 into ensembl
>
> I was looking at rs43469576 a few weeks ago  in dbSNP and I am 99% 
> positive it said on the webpage in big red letters that this snp 
> mapped to 3 genome locations. I checked what ensembl does about this 
> and i have code showing how ensembl too maps it to 3 genome locations
>
>     * chr7(65859978), chr7(91674598), chr6(86134792)
>
> Now when i look at dbSNP it says this variation isn't mapped to any 
> assembly. If i search dbsnp for one of those genome locations (e.g. 
> chr7(65859978)) rs43469576 is no longer in the results
>
> Now i appreciate that I am a fallible human being and could have got 
> confused but it looks to me as if dbSNP has changed and now doesn't 
> seem to show snps as mapping to multiple locations. I looked on their 
> build release notes and schema revisions etc but there is no mention 
> of this. So perhaps i am mistaken. It often happens :)
>
> But regardless of whether i am mistaken or not there still exists a 
> difference between the info in ensembl and dbsnp and I would like to 
> know what to expect from ensembl in the january release. Will i still 
> see a variation like rs43469576 mapped to multiple genome locations or 
> will it be mapped to no assembly.
>
> Which then leads to the next question, what will you get for a 
> variation feature start/end/chromosome if it isn't mapped. As i said 
> at present ensembl seems to map the rs entries in dbSNP that are 
> unmapped so I've not come across it.
>
> thanks a lot
>
>
> _______________________________________________
> Dev mailing list
> Dev at ensembl.org
> http://lists.ensembl.org/mailman/listinfo/dev

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mail.ensembl.org/pipermail/dev_ensembl.org/attachments/20101209/70b9342e/attachment.html>


More information about the Dev mailing list