[ensembl-dev] How to retrieve Global minor allele frequency (MAF) via ensembl ?

[Peter Martin]

Hi ensemblers,
*
I like to compare  the frequency of some observed SNP's against a global
minor allele frequency. I usually do this manually via NCBI / dbSNP.

I.e. i look for rs232 here :
http://www.ncbi.nlm.nih.gov/projects/SNP/snp_ref.cgi?rs=232

and the site reports a MAF of
**MAF/MinorAlleleCount:<http://www.ncbi.nlm.nih.gov/projects/SNP/docs/rs_attributes.html#gmaf>
*A=0.104/228
*
NCBI/dbSNP defines the MAF like this :

**Global minor allele frequency (MAF):**  *dbSNP is reporting the minor
allele frequency for each rs included in  a default global population.
Since this is being provided to distinguish common polymorphism from rare
variants, the MAF is actually the second most frequent allele value. In
other words, if there are 3 alleles, with frequencies of 0.50, 0.49, and
0.01, the MAF will be reported as 0.49. The current default global
population is 1000Genome phase 1 genotype data from 1094 worldwide
individuals, released in the May 2011
<http://www.1000genomes.org/node/506>dataset.


*So here's my question: *Does Ensembl have a similar concept of a *Global
minor allele frequency (MAF) , and if so, how can I retrieve this data via
API ? I don't like to loop trough all allele frequencies and calculate this
for myself...

I had a look the variation tutorial
*www.*ensembl*.org/info/docs/api/variation/variation_tutorial.html
*and at the dev list archive and only came across this (un-answered) post
- http://lists.ensembl.org/pipermail/dev/2010-December/000641.html which
did not help very much.

I also peeked into the sample-table anonymous at ensembldb.ensembl.org :
homo_sapiens_variation_64_37 to check if such freq is maybe stored as a
'global' sample to link between allele frequency but did not find
anything...


Thanks,
    Peter
*
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