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

[Juliano Martins]

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*
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mail.ensembl.org/pipermail/dev_ensembl.org/attachments/20160802/ec3c0bd3/attachment.html>