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<p>Hi Duarte,</p>
<p>We store large scale genotype and frequency data in VCF now, so
you need to set an extra flag on the API:<br>
</p>
<pre class="code sh_perl sh_sourceCode"><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>
<br>
<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>
<div class="moz-cite-prefix"><br>
Best wishes,<br>
<br>
Sarah<br>
<br>
On 06/03/2018 17:00, Duarte Molha wrote:<br>
</div>
<blockquote type="cite"
cite="mid:CAGqkoEKb=mky1uhC8xXkQgms8U4VO1nMavmeNx4h7RncwDMk+Q@mail.gmail.com">
<div dir="ltr">Hi Guys
<div><br>
</div>
<div>I am retrieving variations using the API that have a
certain value of MAF</div>
<div><br>
</div>
<div>for example rs770602</div>
<div><br>
</div>
<div>If you retrieve this variation </div>
<div><br>
</div>
<div>like so: $vf->minor_allele_frequency</div>
<div><br>
</div>
<div>it reports a MAF of 0.495807</div>
<div><br>
</div>
<div>but when I get each allele <br>
<br>
</div>
<div>
<div>my @alleles = @{$vf->get_all_Alleles};</div>
</div>
<div><br>
</div>
<div>and I cycle through them, their frequency is undef</div>
<div><br>
</div>
<div>
<div>foreach my $a (@alleles){</div>
<div><span style="white-space:pre"> </span>my $freq =
$a->frequency();</div>
<div><span style="white-space:pre"> </span>print <span
style="color:rgb(34,34,34);font-family:arial,sans-serif;font-size:small;font-style:normal;font-variant-ligatures:normal;font-variant-caps:normal;font-weight:400;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;background-color:rgb(255,255,255);text-decoration-style:initial;text-decoration-color:initial;float:none;display:inline"><span> </span>$freq;</span></div>
<div>}</div>
</div>
<div><br>
</div>
<div>How do I retrieve the frequency calculated for each
individual alleles on the variation?</div>
<div><br>
</div>
<div>Many thanks</div>
<div><br>
</div>
<div>Duarte<br>
</div>
<div>
</div>
</div>
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</pre>
</blockquote>
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