[ensembl-dev] 1000 genomes frequencies from Ensembl SQL?

[Mark Miller]

Also posted to Biostars https://www.biostars.org/p/200847/



How would I write an SQL query to retrieve all of the frequencies, form all providers, such as seen on a page like http://useast.ensembl.org/Homo_sapiens/Variation/Population?db=core;r=16:89919209-89920209;v=rs1805007;vdb=variation;vf=1232953 ?

Connection info: http://useast.ensembl.org/info/data/mysql.html

I'm especially interested in the 1000 genomes frequencies.

I tried this (among many other queries), but it doesn't seem to include the 1000 Genomes Phase 3 data (for example, the frequency for '1000GENOMES:phase_3:TSI', population ID 373537, should be 0.023 )

SELECT * FROM allele

left join population

on allele.population_id = population.population_id

left join variation

on allele.variation_id = variation.variation_id

where variation.name = 'rs1805007'

  *   Do I need to learn about subsnps?
  *   Is the data masked for privacy? There sure are a lot of NULLs.
  *   Do I just need to keep staring at the Ensembl ERD? Like maybe I need to look in some of the sample or individual tables? http://useast.ensembl.org/info/docs/api/variation/variation_schema.html



Mark Miller
Instem
Head of Bioinformatics & SRS Product Manager
W +1 610 941 0990 x131

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