[ensembl-dev] incorporation of dbSNP 132 into ensembl

Fiona Cunningham fiona at ebi.ac.uk
Thu Dec 9 14:35:18 GMT 2010


 Dear Andrea,

Ensembl currently has data from dbSNP 131 and we will update to dbSNP
132 with release 61 in January. As dbSNP has been updating from
release 131 to release 132 so the differences you have seen may be
explained by this.

Best regards,

Fiona

------------------------------------------------------
Fiona Cunningham
Ensembl Variation Project Leader, EBI
www.ensembl.org
www.lrg-sequence.org
t: 01223 494612 || e: fiona at ebi.ac.uk



On 9 December 2010 14:27, Andrea Edwards <edwardsa at cs.man.ac.uk> 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
>
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