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<p class="MsoNormal"><span style="font-size:11.0pt">Dear Peter,<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt">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
<a href="ftp://ftp.ncbi.nih.gov/snp/organisms/human_9606/VCF/v4.0/00-All.vcf.gz">
ftp://ftp.ncbi.nih.gov/snp/organisms/human_9606/VCF/v4.0/00-All.vcf.gz</a>.<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt">Adam<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt">Adam P. Levine<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt"><o:p> </o:p></span></p>
<p class="MsoNormal"><b><span lang="EN-US" style="font-size:10.0pt;font-family:"Tahoma","sans-serif"">From:</span></b><span lang="EN-US" style="font-size:10.0pt;font-family:"Tahoma","sans-serif""> dev-bounces@ensembl.org [mailto:dev-bounces@ensembl.org]
<b>On Behalf Of </b>Peter Martin<br>
<b>Sent:</b> 24 November 2011 01:46<br>
<b>To:</b> dev@ensembl.org<br>
<b>Subject:</b> [ensembl-dev] How to retrieve Global minor allele frequency (MAF) via ensembl ?<o:p></o:p></span></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal"><br>
Hi ensemblers, <br>
<br>
<strong><span style="font-weight:normal">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.
</span></strong><br>
<br>
<strong><span style="font-weight:normal">I.e. i look for rs232 here : <a href="http://www.ncbi.nlm.nih.gov/projects/SNP/snp_ref.cgi?rs=232">
http://www.ncbi.nlm.nih.gov/projects/SNP/snp_ref.cgi?rs=232</a></span></strong><br>
<br>
<strong><span style="font-weight:normal">and the site reports a MAF of </span><a href="http://www.ncbi.nlm.nih.gov/projects/SNP/docs/rs_attributes.html#gmaf">MAF/MinorAlleleCount:</a></strong>A=0.104/228
<br>
<br>
<strong><span style="font-weight:normal">NCBI/dbSNP defines the MAF like this : </span>
</strong><br>
<br>
<strong>Global minor allele frequency (MAF): </strong>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 <a href="http://www.1000genomes.org/node/506">May 2011</a> dataset.
<br>
<br>
<br>
<strong><span style="font-weight:normal">So here's my question: </span></strong>Does Ensembl have a similar concept of a
<strong>Global minor allele frequency (MAF) </strong><strong><span style="font-weight:normal">, 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...
</span></strong><br>
<br>
<strong><span style="font-weight:normal">I had a look the variation tutorial </span>
</strong><cite><a href="http://www.ensembl.org/info/docs/api/variation/variation_tutorial.html"><span style="font-style:normal">www.</span><b><span style="font-style:normal">ensembl</span></b><span style="font-style:normal">.org/info/docs/api/variation/variation_tutorial.html</span></a>
</cite><strong><span style="font-weight:normal">and at the dev list archive and only came across this (un-answered) post -
<a href="http://lists.ensembl.org/pipermail/dev/2010-December/000641.html">http://lists.ensembl.org/pipermail/dev/2010-December/000641.html</a> which did not help very much.
</span></strong><br>
<br>
<strong><span style="font-weight:normal">I also peeked into the sample-table <a href="mailto:anonymous@ensembldb.ensembl.org">
anonymous@ensembldb.ensembl.org</a> : 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...
</span></strong><br>
<br>
<b><br>
</b><strong><span style="font-weight:normal">Thanks, </span></strong><br>
<strong><span style="font-weight:normal"> Peter</span></strong><o:p></o:p></p>
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