Retrieve All Population Frequency Data For A Snp In 1000Genomes Phase_1

Question

[haansi]

Hi all!

Just found this entry: Retrieving All Available Frequency Data For A Snp Using Ensembl Api Tools which is very close to what i need. Similar to Krisr I would like to retrieve all population frequency data available from 1000Genomes phase 1 for a SNP, if possible via SQL.

Ensembls Biomart provides minor allele information for the ALL superpopulation only. Pierre Lindenbaum's solution is almost getting me to the desired result - but when I run the sql statement (on homosapiensvariation6937), I only get results from 1000Genoms:pilot_1 - not from phase1.

select distinct V.name, S.handle, A.frequency, M.name, F.allele_string
  from (  allele as A,   variation as V,   subsnp_handle as S,  variation_feature as F  ) left join  sample as M
  on (M.sample_id = A.sample_id ) 
    where 
        V.variation_id=A.variation_id and
        S.subsnp_id =A.subsnp_id and
        F.variation_id=V.variation_id and 
        V.name="rs3"
      order by 2;

Any suggestions where I could find this data? Alternatively: is there a way to get the sql statements from bioperl - since Bert Overduin provided a nice perl-script (need sql for my workflow) ?

Answer 1

[Peixe]

Maybe dbSNP-Q could be useful...

Lets you make a query to dbSNP, 1KG, HapMap and more all-in-one through simple mySQL queries or customized ones.

[haansi]

Hi Peixe! Thank you very much for this very interesting web-app!! Just gave it a try - unfortunately there's only data from 1000Genomes Pilot 1 not but not from 1000Genomes Phase 1. Otherwise a very cool and fast application!

Answer 2

[Zev.Kronenberg]

This isn't an SQL solution but it will do the trick.

use tabix and point it at this file:

http://ftp.1000genomes.ebi.ac.uk/vol1/ftp/phase1/analysis_results/integrated_call_sets/ALL.wgs.integrated_phase1_v3.20101123.snps_indels_sv.sites.vcf.gz

#CHROM  POS     ID      REF     ALT     QUAL    FILTER  INFO
1       10523   .       TCCG    T       152     PASS    VT=INDEL;RSQ=0.5246;ERATE=0.0023;AN=2184;AA=.;THETA=0.0172;AC=5;AVGPOST=0.9954;LDAF=0.0045;AF=0.00;AMR_AF=0.00;AFR_AF=0.01

AF= global allele freq

AMR_AF = AMR population

ect...

[haansi]

Hi Zev! Thank you very much for your answer! Found this approach also in a previous question (Getting Allele Frequencies From 1000 Genomes. Wasn't aware of the ftp file you mentioned though. I gave it a try, the query time was about 5 seconds (could live with it), but I need all informtions to frequencys as here in the 1000 Genomes table for my pipeline (just an example with a random snp) : http://www.ensembl.org/Homo_sapiens/Variation/Population?db=core;r=12:51419664-51420664;v=rs6580779;vdb=variation;vf=4447658 Are there other locations for querying?

[Zev.Kronenberg]

The file is only a couple gigs (~2?). You could just download it and use tabix locally. The tabix index scheme makes querying trivial and very very fast.