<html><head><meta http-equiv="Content-Type" content="text/html; charset=utf-8"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class="">The files are described in a config file: <a href="https://github.com/Ensembl/ensembl-variation/blob/release/91/modules/Bio/EnsEMBL/Variation/DBSQL/vcf_config.json" class="">https://github.com/Ensembl/ensembl-variation/blob/release/91/modules/Bio/EnsEMBL/Variation/DBSQL/vcf_config.json</a><div class=""><br class=""></div><div class="">You don’t need to have the files locally. The files are all availably remotely. If you want to keep your files locally you need to download the files and update the vcf_config,json with the new location.</div><div class=""><br class=""></div><div class="">HTH,</div><div class="">Anja</div><div class=""><div><br class=""><blockquote type="cite" class=""><div class="">On 6 Mar 2018, at 17:56, Duarte Molha <<a href="mailto:duartemolha@gmail.com" class="">duartemolha@gmail.com</a>> wrote:</div><br class="Apple-interchange-newline"><div class=""><div dir="ltr" class="">I think that just introduced a can of worms into my script. Where are these VCF files stored? I am running the code from a locally stored ensembl database.<div class=""><br class=""></div><div class="">Do I need to retrieve additional data when creating my database to get these files?</div><div class=""><br class=""></div><div class="">Thanks</div><div class=""><br class=""></div><div class="">Duarte</div></div><div class="gmail_extra"><br clear="all" class=""><div class=""><div class="gmail_signature" data-smartmail="gmail_signature"><div dir="ltr" class=""><div class=""><table border="0" cellpadding="0" cellspacing="0" style="margin:0px;padding:0px;border:0px;outline:0px;font-size:14px;font-family:proxima-nova-1,proxima-nova-2,Tahoma,Helvetica,Verdana,sans-serif;vertical-align:baseline;border-spacing:0px;color:rgb(51,51,51);line-height:18.2000007629395px" class=""><tbody style="margin:0px;padding:0px;border:0px;outline:0px;font-weight:inherit;font-style:inherit;font-family:inherit;vertical-align:baseline" class=""><tr 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style="margin:0px;padding:0px;border:0px;outline:0px;font-weight:inherit;font-style:inherit;font-family:inherit;vertical-align:baseline;color:rgb(43,130,173);text-decoration:none;display:inline-block" target="_blank" class=""><table border="0" cellpadding="0" cellspacing="0" style="margin:0px;padding:0px;border:0px;outline:0px;font-weight:inherit;font-style:inherit;font-family:inherit;vertical-align:baseline;border-spacing:0px" class=""><tbody style="margin:0px;padding:0px;border:0px;outline:0px;font-weight:inherit;font-style:inherit;font-family:inherit;vertical-align:baseline" class=""><tr style="margin:0px;padding:0px;border:0px;outline:0px;font-weight:inherit;font-style:inherit;font-family:inherit;vertical-align:baseline" class=""><td align="left" valign="top" style="padding:0px;border:0px;outline:0px;font-style:inherit;font-family:inherit;vertical-align:top;width:auto;line-height:1" class=""><img alt="--" width="0" height="0" style="margin:0px;padding:0px;border:0px;outline:0px;font-weight:inherit;font-style:inherit;font-family:inherit;vertical-align:baseline;display:block;width:0px;height:0px;overflow:hidden" class=""><div style="margin:0px;padding:0px;border:0px;outline:0px;font-weight:bold;font-style:inherit;font-size:18px;font-family:proxima-nova-1,Proxima-Nova,Helvetica,Arial,sans-serif;vertical-align:baseline;line-height:1;color:rgb(51,51,51)" class="">Duarte Molha</div><div style="margin:3px 0px 0px;padding:0px;border:0px;outline:0px;font-weight:inherit;font-style:inherit;font-size:12px;font-family:proxima-nova-1,Proxima-Nova,Helvetica,Arial,sans-serif;vertical-align:baseline" class=""><img alt="https://" width="0" height="0" style="margin:0px;padding:0px;border:0px;outline:0px;font-weight:inherit;font-style:inherit;font-family:inherit;vertical-align:baseline;display:block;width:0px;height:0px;overflow:hidden" class="">about.me/duarte</div></td></tr><tr 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<br class=""><div class="gmail_quote">On 6 March 2018 at 17:16, Sarah Hunt <span dir="ltr" class=""><<a href="mailto:seh@ebi.ac.uk" target="_blank" class="">seh@ebi.ac.uk</a>></span> wrote:<br class=""><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<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="m_-6538029127110316456sh_perl m_-6538029127110316456code m_-6538029127110316456sh_sourceCode"><span class="m_-6538029127110316456sh_variable">$variation_adaptor</span><span class="m_-6538029127110316456sh_symbol">-></span><span class="m_-6538029127110316456sh_function">db</span><span class="m_-6538029127110316456sh_symbol">-></span><span class="m_-6538029127110316456sh_function">use_<wbr class="">vcf</span><span class="m_-6538029127110316456sh_symbol">(</span><span class="m_-6538029127110316456sh_number">1</span><span class="m_-6538029127110316456sh_symbol">);
</span></pre>
to access it. More details are available here:<br class="">
<br class="">
<a class="m_-6538029127110316456moz-txt-link-freetext" href="http://www.ensembl.org/info/docs/api/variation/variation_tutorial.html#ag" target="_blank">http://www.ensembl.org/info/<wbr class="">docs/api/variation/variation_<wbr class="">tutorial.html#ag</a><br class="">
<div class="m_-6538029127110316456moz-cite-prefix"><br class="">
Best wishes,<br class="">
<br class="">
Sarah<div class=""><div class="h5"><br class="">
<br class="">
On 06/03/2018 17:00, Duarte Molha wrote:<br class="">
</div></div></div>
<blockquote type="cite" class=""><div class=""><div class="h5">
<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: $vf->minor_allele_<wbr class="">frequency</div>
<div class=""><br class="">
</div>
<div class="">it reports a MAF of 0.495807</div>
<div class=""><br class="">
</div>
<div class="">but when I get each allele <br class="">
<br class="">
</div>
<div class="">
<div class="">my @alleles = @{$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-wrap" class=""> </span>my $freq =
$a->frequency();</div>
<div class=""><span style="white-space:pre-wrap" class=""> </span>print <span style="color:rgb(34,34,34);font-family:arial,sans-serif;font-size:small;font-style:normal;font-variant-ligatures:normal;font-variant-caps:normal;font-weight:400;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;background-color:rgb(255,255,255);text-decoration-style:initial;text-decoration-color:initial;float:none;display:inline" class=""><span class=""> </span>$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="m_-6538029127110316456mimeAttachmentHeader"></fieldset>
<br class="">
</div></div><pre class="">______________________________<wbr class="">_________________
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</pre>
</blockquote>
<br class="">
</div>
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