[ensembl-dev] Working on synonymous variations with the API

Jerome Dauvillier jerome.dauvillier at isb-sib.ch
Fri May 2 15:12:26 BST 2014


Crisp and clear - Thanks a lot !

Jérôme Dauvillier
SIB | Swiss Institute of Bioinformatics
  

Le 02/05/14 16:07, Will McLaren a écrit :
> Hello,
>
> We keep a record of merged rsIDs in the variation_synonym table of our 
> database.
>
> When you do a look-up by rsID, e.g.
>
> my $variation = $variation_adaptor->fetch_by_name('rs7335199');
>
> the API checks both the variation (for the primary ID) and 
> variation_synonym (for the archived IDs).
>
> In the above example this will actually return the variation object 
> corresponding to rs3, to which it has been merged.
>
> Once you have the variation object you can ask for synonyms (i.e. all 
> of the archived IDs) with the following call:
>
> my @synonyms = @{$variation->get_all_synonyms()};
>
> To limit this to just rsIDs, for example, add the source 'dbSNP' as an 
> argument:
>
> my @rs_synonyms = @{$variation->get_all_synonyms('dbSNP')};
>
> In the example, both of these lists will then contain the archived 
> rsID that you initially searched for.
>
> We do not retain variation_feature records corresponding to archived 
> rsIDs, since they are considered to be merged with the primary rsID's 
> variation_feature(s).
>
> Hope that helps
>
> Will McLaren
> Ensembl Variation
>
>
> On 2 May 2014 14:56, Jerome Dauvillier <jerome.dauvillier at isb-sib.ch 
> <mailto:jerome.dauvillier at isb-sib.ch>> wrote:
>
>     Hi Ensembl dev,
>
>     Is there some support in the API for
>     - Detecting a rs-ID refers to a synonymous variation ?
>     - Given the rs-ID of a synonymous variation, getting the variation
>     it was merged into, and the corresponding variation feature object ?
>
>     Many thanks in advance !
>
>     Best,
>
>     -- 
>     Jérôme Dauvillier
>     SIB | Swiss Institute of Bioinformatics
>
>
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