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<div class="moz-cite-prefix">Hello Will,<br>
<br>
Thank you for the information.<br>
<br>
Best regards,<br>
Guillermo.<br>
<br>
On 11/05/2013 03:39 PM, Will McLaren wrote:<br>
</div>
<blockquote
cite="mid:CAMVEDX0Xrx0eT7EztPdNY5xpOFcXo3ngbi73SDH3eKGNBeJykQ@mail.gmail.com"
type="cite">
<div dir="ltr">Hi Guillermo,
<div><br>
</div>
<div>I assume by "wild-type" you mean the most common or major
allele?</div>
<div><br>
</div>
<div>The minor allele is listed by the VEP when you use --gmaf,
as well as in our Ensembl MySQL databases, along with the
allele string (the list of all alleles) so it should be fairly
trivial to work out which is the major or wild-type allele
from that information.</div>
<div><br>
</div>
<div>You will see rare cases where there are more than two
alleles in the allele string; in this case you could assume
that the first allele in the allele string is the one you want
(since we put the reference allele first in this string where
we can).</div>
<div><br>
</div>
<div>You could do this in a plugin for the VEP, or extract the
data from the MySQL table and run a quick script over it.</div>
<div><br>
</div>
<div>In a plugin you'd need to access the
$tva->variation_feature->{existing} data structure to
see the fields you require.</div>
<div><br>
</div>
<div>Regards</div>
<div><br>
</div>
<div>Will McLaren</div>
<div>Ensembl Variation</div>
</div>
<div class="gmail_extra"><br>
<br>
<div class="gmail_quote">On 5 November 2013 14:18, Guillermo
Marco Puche <span dir="ltr"><<a moz-do-not-send="true"
href="mailto:guillermo.marco@sistemasgenomicos.com"
target="_blank">guillermo.marco@sistemasgenomicos.com</a>></span>
wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0
.8ex;border-left:1px #ccc solid;padding-left:1ex">
<div bgcolor="#FFFFFF" text="#000066"> Dear devs,<br>
<br>
I know at this moment VEP script offers population
frecuencies from 1000 genomes project, which is awesome.<br>
<br>
I would like to know if it's possible to retrieve the
"wild-type allele" from 1000 genomes project for each
variation position. As you may know variation allele may
be biased due to the human reference we use (it's very
uncommon but it does happen). <br>
<br>
I don't know if this information is included in ensembl
database or is going to be introduceded in near future.<br>
<br>
<br>
Thank you.<br>
<br>
Best regards,<br>
Guillermo.<br>
</div>
<br>
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</blockquote>
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