<div dir="ltr">Hi Duarte,<div><br></div><div style>This would only really work with the GMAF, since that is the only one for which the allele is provided.</div><div style><br></div><div style>The other frequencies (at least those stored in the cache) are specifically the minor allele frequency - the particular allele to which this refers is not stored, so your idea would not work, or at least not reliably.</div>
<div style><br></div><div style>If retrieving frequencies from the database, you can get the allele, but this is very slow for large datasets so I don't think it would be worth implementing.</div><div style><br></div>
<div style>You could always jump in with a plugin - all of the frequency stuff you'll find cached on the variation_feature object in various hash structures - just dump one out in the debugger and you'll see the structure.</div>
<div style><br></div><div style>Will</div></div><div class="gmail_extra"><br><br><div class="gmail_quote">On 23 May 2013 09:26, Duarte Molha <span dir="ltr"><<a href="mailto:Duarte.Molha@ogt.com" target="_blank">Duarte.Molha@ogt.com</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div lang="EN-GB" link="blue" vlink="purple"><div><p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d">Any views on this?<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d"><u></u> <u></u></span></p><p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d">Thanks<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d"><br>Duarte<u></u><u></u></span></p><p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d"><u></u> <u></u></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d"><u></u> <u></u></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""> <a href="mailto:dev-bounces@ensembl.org" target="_blank">dev-bounces@ensembl.org</a> [mailto:<a href="mailto:dev-bounces@ensembl.org" target="_blank">dev-bounces@ensembl.org</a>] <b>On Behalf Of </b>Duarte Molha<br>
<b>Sent:</b> 22 May 2013 13:17<br><b>To:</b> Ensembl<br><b>Subject:</b> Re: [ensembl-dev] Feature request (Allele variant Frequency)<u></u><u></u></span></p><div><div class="h5"><p class="MsoNormal"><u></u> <u></u></p><div>
<p class="MsoNormal">Also, in addition to this, I could probably use the frequency flags to they all information i need and then parse it later on...<u></u><u></u></p><div><p class="MsoNormal"><u></u> <u></u></p></div><div>
<p class="MsoNormal">like <u></u><u></u></p></div><div><p class="MsoNormal"><u></u> <u></u></p></div><div><div><p class="MsoNormal">check_frequency 1<u></u><u></u></p></div><div><p class="MsoNormal">freq_filter include<u></u><u></u></p>
</div><div><p class="MsoNormal">freq_freq 1<u></u><u></u></p></div><div><p class="MsoNormal">freq_gt_lt lt<u></u><u></u></p></div><div><p class="MsoNormal">freq_pop any<u></u><u></u></p>
</div></div><div><p class="MsoNormal"><u></u> <u></u></p></div><div><p class="MsoNormal">However, this is cumbersome and also removes all other variants from the output that have no frequency information.<u></u><u></u></p>
</div><div><p class="MsoNormal"><u></u> <u></u></p></div><div><p class="MsoNormal">Thanks<u></u><u></u></p></div><div><p class="MsoNormal"><u></u> <u></u></p></div><div><p class="MsoNormal">Duarte<u></u><u></u></p></div></div>
<div><p class="MsoNormal"><br clear="all"><u></u><u></u></p><div><p class="MsoNormal"><span style="color:#999999;background:white">=========================<br> Duarte Miguel Paulo Molha </span><u></u><u></u></p>
<div><p class="MsoNormal"><span style="color:#999999;background:white"> <a href="http://about.me/duarte" target="_blank">http://about.me/duarte</a> <br>=========================</span><u></u><u></u></p></div>
</div><p class="MsoNormal" style="margin-bottom:12.0pt"><u></u> <u></u></p><div><p class="MsoNormal">On Wed, May 22, 2013 at 11:57 AM, Duarte Molha <<a href="mailto:duartemolha@gmail.com" target="_blank">duartemolha@gmail.com</a>> wrote:<u></u><u></u></p>
<div><div><p class="MsoNormal">I am not sure if you have already addressed this question Will<u></u><u></u></p></div><div><p class="MsoNormal">But I would like to request that a additional option be included for annotation output.<u></u><u></u></p>
</div><div><p class="MsoNormal"><u></u> <u></u></p></div><div><p class="MsoNormal">Currently the GMAF of a given known variation is output with the --GMAF flag<u></u><u></u></p></div><div><p class="MsoNormal"><u></u> <u></u></p>
</div><div><p class="MsoNormal">However, this does not give us the frequency of the seen allele on out sample.<u></u><u></u></p></div><div><p class="MsoNormal"><u></u> <u></u></p></div><div><p class="MsoNormal">say their is a variation <u></u><u></u></p>
</div><div><p class="MsoNormal"><u></u> <u></u></p></div><div><p class="MsoNormal">like so<u></u><u></u></p></div><div><p class="MsoNormal">ref_allele alt_alleles<u></u><u></u></p></div><div><p class="MsoNormal">C A,T<u></u><u></u></p>
</div><div><p class="MsoNormal"><u></u> <u></u></p></div><div><p class="MsoNormal">And our sample has a genotype 1,2<u></u><u></u></p></div><div><p class="MsoNormal">and the GMAF gives us GMAF=A:0.2399<u></u><u></u></p></div>
<div><p class="MsoNormal"><u></u> <u></u></p></div><div><p class="MsoNormal">In this case it is not possible to determine the allelic frequency of the other allele present in the sample.<u></u><u></u></p></div><div><p class="MsoNormal">
<u></u> <u></u></p></div><div><p class="MsoNormal">Ideally there should be a flag like --allele_freq that would five you the allele for the allele present in the sample.<u></u><u></u></p></div><div><p class="MsoNormal">You must already be calculating this because you have fields for filtering variation based on their frequency in any given population ,<u></u><u></u></p>
</div><div><p class="MsoNormal"><u></u> <u></u></p></div><div><p class="MsoNormal">Best regards<u></u><u></u></p></div><div><p class="MsoNormal"><u></u> <u></u></p></div><div><p class="MsoNormal">Duarte<u></u><u></u></p></div>
<p class="MsoNormal"><br clear="all"><u></u><u></u></p><div><p class="MsoNormal"><span style="color:#999999">=========================<br> Duarte Miguel Paulo Molha </span><u></u><u></u></p><div><p class="MsoNormal">
<span style="color:#999999"> <a href="http://about.me/duarte" target="_blank">http://about.me/duarte</a> <br>=========================</span><u></u><u></u></p></div></div></div></div><p class="MsoNormal"><u></u> <u></u></p>
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