[ensembl-dev] Where I get he same data like REST API to variation with genotype population?

[Will McLaren]

Hi Juliano,

Due to the large number of positions and alleles, we don't store allele
frequencies for 1000 Genomes data in our MySQL schema.

Instead, the REST API and web interfaces use our Perl API [1], which
includes a layer that queries VCF files containing genotype data and
calculates these frequencies on the fly [2].

If you have variant positions in addition to the rsIDs, you might like to
consider using the Variant Effect Predictor [3]. This tool is designed to
rapidly analyse many variants, and is able to annotate such positions with
frequency data from 1000 Genomes, ExAC and more [4]. While it can accept
rsIDs as input, it works most efficiently if you use something like a VCF
containing the variant's genomic coordinates.

Hope that helps

Will McLaren
Ensembl Variation

[1] : http://www.ensembl.org/info/docs/api/index.html
[2] :
http://www.ensembl.info/blog/2015/06/18/1000-genomes-phase-3-frequencies-genotypes-and-ld-data/
[3] : http://www.ensembl.org/vep
[4] :
http://www.ensembl.org/info/docs/tools/vep/script/vep_options.html#opt_gmaf

On 3 August 2016 at 10:28, Kieron Taylor <ktaylor at ebi.ac.uk> wrote:

> Dear Juliano,
>
> You are correct, that requesting millions of variants at 15 per second
> would take a very long time. This is why we support batch requests via POST.
>
> https://rest.ensembl.org/documentation/info/variation_post
>
> You can greatly increase your throughput by putting hundreds of IDs in
> each request, for example:
>
> curl 'https://rest.ensembl.org/variation/homo_sapiens' -H
> 'Content-type:application/json' -H 'Accept:application/json' -X POST -d '{
> "ids" : ["rs56116432", "COSM476", .... ] }'
>
> If that is not suitable (run time measured in a few hours perhaps), we
> have the original Variation API which can undoubtedly help you get the data
> directly. Someone from our helpdesk or Variation team might be able to help
> if you still feel you must query the database directly.
>
> Regards,
>
> Kieron
>
>
> Kieron Taylor PhD.
> Ensembl Developer
>
> EMBL, European Bioinformatics Institute
>
>
>
>
>
>
> > On 2 Aug 2016, at 20:51, Juliano Martins <julianovmartins at gmail.com>
> wrote:
> >
> > Hello,
> >
> > I am Brazilian student of computer science at the Catholic University of
> Paraná. I am starting research on genome variants and would like to extract
> some statistics such data and for that I need to download it to my local
> machine.
> >
> > Using the REST API (
> >
> https://rest.ensembl.org/variation/human/rs56116432?content-type=application/json;population_genotypes=1)
> I get exactly the data I need, but it would be very time consuming for
> millions of variants IDs because the service time limits.
> >
> > Where I could get the same information (range, population, genotype )
> massively?
> >
> > I tried to find this data into the public mysql ensembl database and
> performed several queries, but did not get the same data. Especially the
> 'population' table and frequency fields does not seems to have the same
> data I got the in the REST API.
> >
> > I need data variation for the assembly GRCh37 3 GRCh38 and looked for
> these two bases:
> > - homo_sapiens_variation_73_37
> > - homo_sapiens_variation_85_38
> >
> >
> > This is a sample query that I used in the database
> (homo_sapiens_variation_73_37):
> >
> > SELECT DISTINCT
> > variation.name,
> > allele.frequency,
> > allele.count,
> > allele_code.allele,
> > variation.ancestral_allele,
> > variation.minor_allele,
> > variation.minor_allele_freq,
> > variation.minor_allele_count,
> > population.name
> > FROM allele, allele_code, variation, population
> > WHERE variation.name LIKE 'rs56116432' AND
> > allele.allele_code_id = allele_code.allele_code_id AND
> > allele.variation_id = variation.variation_id AND
> > allele.population_id = population.population_id
> >
> > I thank you!.
> > Sorry my bad English.
> >
> > Juliano V. Martins
> > _______________________________________________
> > Dev mailing list    Dev at ensembl.org
> > Posting guidelines and subscribe/unsubscribe info:
> http://lists.ensembl.org/mailman/listinfo/dev
> > Ensembl Blog: http://www.ensembl.info/
>
>
> _______________________________________________
> Dev mailing list    Dev at ensembl.org
> Posting guidelines and subscribe/unsubscribe info:
> http://lists.ensembl.org/mailman/listinfo/dev
> Ensembl Blog: http://www.ensembl.info/
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mail.ensembl.org/pipermail/dev_ensembl.org/attachments/20160803/cc079932/attachment.html>