[ensembl-dev] variation api - mapping between dbsnp and ensembl

Will McLaren wm2 at ebi.ac.uk
Tue Nov 30 13:13:08 GMT 2010


Hi Andrea,

The version of dbSNP is stored in the source table; you can also
access it through the API from the variation adaptor using the method
call:

$variation_adaptor->get_source_version('dbSNP');

The source description for dbSNP also contains information on if it
has been remapped; this is accessed via a variation object:

$variation->source_description()

If it has been remapped the description will contain a string e.g.
"[remapped from build 7]" is what we have for zebrafish currently. Cow
is on the same build as dbSNP's DB (build 4), so no remapping was
done.

Will


On 30 November 2010 13:00, Andrea Edwards <edwardsa at cs.man.ac.uk> wrote:
> Hello
>
> I have written a small script to get all of the known snps for cow from
> ensembl. I have been told the only variation data for cow in ensembl is from
> dbSNP
>
> Questions
> 1. How do i know which build of dbsnp is used in a particular ensembl build?
> I have not been able to find any release information for the external
> databases used by a particular ensembl release
>
> 2. How do i know that the genome build of the variation in dbsnp is the same
> as the genome build in ensembl. If i look at a cow snp in dbsnp it tells me
> what genome build it is associated with. What happens if the ensembl
> database is mapped to a different genome assembly than dbSNP?
>
> thanks
>
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