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

[Fiona Cunningham]

 Dear Peter,

This is a new feature that dbSNP/NCBI have started to produce since
their release of dbSNP 134 sometime late in August. It takes a little
while for ensembl to catch up with the large data release dbSNP
provides but you should see this information in our next ensembl
release (release 65) coming out in early December.

If you have any more questions, do not hesitate to ask.

Best wishes,

Fiona

-----------------------------------------------------------------------------------
Fiona Cunningham
Ensembl Coordinator, Ensembl Variation Project Leader.
EMBL-EBI, Genome Campus, Hinxton, UK
www.ensembl.org || www.lrg-sequence.org
fiona at ebi.ac.uk   || t: +44 1223 494612



On 24 November 2011 01:45, Peter Martin <mpeter908 at gmail.com> wrote:
>
> 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: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 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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