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

Will McLaren wm2 at ebi.ac.uk
Fri May 2 15:07:26 BST 2014


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> 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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