<html><head><meta http-equiv="Content-Type" content="text/html; charset=us-ascii"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class="">Hi Duarte,<div class=""><br class=""></div><div class="">here is also some example code: </div><div class=""><br class=""></div><div class=""><div class="">my $va = $registry->get_adaptor('human', 'variation', 'variation');</div><div class="">$va->db->use_vcf(1);</div><div class="">my $variation = $va->fetch_by_name('rs770602');</div><div class=""><br class=""></div><div class="">my @alleles = @{$variation->get_all_Alleles};</div><div class=""><br class=""></div><div class="">foreach my $a (@alleles){</div><div class=""> my $freq = $a->frequency;</div><div class=""> if (defined $freq) {</div><div class=""> my $allele = $a->allele;</div><div class=""> my $population = (defined $a->population) ? $a->population->name : 'NA';</div><div class=""> print $population, ' ', $allele, ' ', $freq, "\n";</div><div class=""> }</div><div class="">}</div><div class=""><br class=""></div></div><div class="">More information on the Allele object is here <a href="http://www.ensembl.org/info/docs/Doxygen/variation-api/classBio_1_1EnsEMBL_1_1Variation_1_1Allele.html" class="">http://www.ensembl.org/info/docs/Doxygen/variation-api/classBio_1_1EnsEMBL_1_1Variation_1_1Allele.html</a></div><div class=""><br class=""></div><div class="">HTH,</div><div class="">Anja<br class=""><div><br class=""><blockquote type="cite" class=""><div class="">On 6 Mar 2018, at 17:16, Sarah Hunt <<a href="mailto:seh@ebi.ac.uk" class="">seh@ebi.ac.uk</a>> wrote:</div><br class="Apple-interchange-newline"><div class="">
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" class="">
<div bgcolor="#FFFFFF" text="#000000" class=""><p class=""><br class="">
</p><p class="">Hi Duarte,</p><p class="">We store large scale genotype and frequency data in VCF now, so
you need to set an extra flag on the API:<br class="">
</p>
<pre class="sh_perl sh_sourceCode code"><span class="sh_variable">$variation_adaptor</span><span class="sh_symbol">-></span><span class="sh_function">db</span><span class="sh_symbol">-></span><span class="sh_function">use_vcf</span><span class="sh_symbol">(</span><span class="sh_number">1</span><span class="sh_symbol">);
</span></pre>
to access it. More details are available here:<br class="">
<br class="">
<a class="moz-txt-link-freetext" href="http://www.ensembl.org/info/docs/api/variation/variation_tutorial.html#ag">http://www.ensembl.org/info/docs/api/variation/variation_tutorial.html#ag</a><br class="">
<div class="moz-cite-prefix"><br class="">
Best wishes,<br class="">
<br class="">
Sarah<br class="">
<br class="">
On 06/03/2018 17:00, Duarte Molha wrote:<br class="">
</div>
<blockquote type="cite" cite="mid:CAGqkoEKb=mky1uhC8xXkQgms8U4VO1nMavmeNx4h7RncwDMk+Q@mail.gmail.com" class="">
<div dir="ltr" class="">Hi Guys
<div class=""><br class="">
</div>
<div class="">I am retrieving variations using the API that have a
certain value of MAF</div>
<div class=""><br class="">
</div>
<div class="">for example rs770602</div>
<div class=""><br class="">
</div>
<div class="">If you retrieve this variation </div>
<div class=""><br class="">
</div>
<div class="">like so: $vf->minor_allele_frequency</div>
<div class=""><br class="">
</div>
<div class="">it reports a MAF of 0.495807</div>
<div class=""><br class="">
</div>
<div class="">but when I get each allele <br class="">
<br class="">
</div>
<div class="">
<div class="">my @alleles = @{$vf->get_all_Alleles};</div>
</div>
<div class=""><br class="">
</div>
<div class="">and I cycle through them, their frequency is undef</div>
<div class=""><br class="">
</div>
<div class="">
<div class="">foreach my $a (@alleles){</div>
<div class=""><span style="white-space:pre" class=""> </span>my $freq =
$a->frequency();</div>
<div class=""><span style="white-space:pre" class=""> </span>print <span style="color:rgb(34,34,34);font-family:arial,sans-serif;font-size:small;font-style:normal;font-variant-ligatures:normal;font-variant-caps:normal;font-weight:400;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;background-color:rgb(255,255,255);text-decoration-style:initial;text-decoration-color:initial;float:none;display:inline" class=""><span class=""> </span>$freq;</span></div>
<div class="">}</div>
</div>
<div class=""><br class="">
</div>
<div class="">How do I retrieve the frequency calculated for each
individual alleles on the variation?</div>
<div class=""><br class="">
</div>
<div class="">Many thanks</div>
<div class=""><br class="">
</div>
<div class="">Duarte<br class="">
</div>
<div class="">
</div>
</div>
<br class="">
<fieldset class="mimeAttachmentHeader"></fieldset>
<br class="">
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</pre>
</blockquote>
<br class="">
</div>
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