[ensembl-dev] VEP RSid mergers

[Will McLaren]

Hi Duarte,

dbSNP have fixed this entry since we imported it. The next time we import
from dbSNP the merge will be picked up and the higher rs will be given as a
synonym for the lower.

There's no existing flag, but you could process the data with a plugin.
Existing variants are cached on the variation feature object.

There is a need for caution here - for example, if a deletion and a SNP are
co-located, you won't be able to distinguish between the two based on the
rsID alone; you should use --check_alleles to ensure that the VEP only
reports an existing variation if the alleles match exactly to your input.

Regards

Will


On 24 May 2013 10:27, Duarte Molha <duartemolha at gmail.com> wrote:

> Dear Developers
>
> I have a variant that I annotated using VEP at position
> 2_3504687_A/G Genotype 0/1
>
> when annotating this I get 2 RS ids on the Existing_variation field :
>
> rs9950,rs17350005
>
> in dbSNP , the latter has been merged back into the former, but in ENSEMBL
> there is no such indication.
>
> http://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?rs=rs17350005
>
>
> http://www.ensembl.org/Homo_sapiens/Variation/Summary?db=core;r=2:3504187-3505187;v=rs17350005;vdb=variation;vf=9931714
>
> Also the synonyms field is empty  and I would expect, it they are in fact
> the same variation, then the rs9950 should be a  synonym for rs17350005,
> correct?
>
>  Is there a flag  could use so that I could disregard the latter RSid
> (maybe using a plugin) ?
>
> Best regards
>
> Duarte
>
>
> =========================
>      Duarte Miguel Paulo Molha
>          http://about.me/duarte
> =========================
>
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