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

[A. P. Levine]

Dear Peter,

If you simply want to extract the GMAF for a number of SNPs without having to search for each online you can extract them from ftp://ftp.ncbi.nih.gov/snp/organisms/human_9606/VCF/v4.0/00-All.vcf.gz.

Adam

Adam P. Levine

From: dev-bounces at ensembl.org [mailto:dev-bounces at ensembl.org] On Behalf Of Peter Martin
Sent: 24 November 2011 01:46
To: dev at ensembl.org
Subject: [ensembl-dev] How to retrieve Global minor allele frequency (MAF) via ensembl ?


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<http://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<mailto: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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