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Dear Manuel,<br>
<br>
This plugin uses data structures created by VEP to provide
additional information, so it would not be trivial to adapt it to
annotate input from a different program. <br>
<br>
Assuming you are using ensembl transcripts, there is an example in
the variation tutorial: <br>
<br>
<a class="moz-txt-link-freetext" href="http://www.ensembl.org/info/docs/api/variation/variation_tutorial.html">http://www.ensembl.org/info/docs/api/variation/variation_tutorial.html</a><br>
<br>
which may help you in creating the VariationFeature and
TranscriptVariations objects required by the plugin from a novel
input. <br>
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<br>
Best wishes,<br>
<br>
Sarah<br>
<br>
<div class="moz-cite-prefix">On 07/07/2014 12:37, Manuel Tardáguila
Sancho wrote:<br>
</div>
<blockquote
cite="mid:20140707113759.57FE713298A_3BA8697B@hx-mx2.ebi.ac.uk"
type="cite">
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<div dir="ltr"><span style="color: rgb(68, 68, 68); font-size:
15px; line-height: 21.299999237060547px; background-color:
rgb(255, 255, 255);">To whom it may concern,</span>
<div style="line-height: 21.299999237060547px; color: rgb(68,
68, 68); font-size: 15px; background-color: rgb(255, 255,
255);"><br>
</div>
<div style="line-height: 21.299999237060547px; color: rgb(68,
68, 68); font-size: 15px; background-color: rgb(255, 255,
255);">My name is Manuel Tardaguila and I am an MSC in
bioinformatics doing a project in the university of Lausanne.
I am working on annotated variations using VEP and snpEff as
annotators.</div>
<div style="line-height: 21.299999237060547px; color: rgb(68,
68, 68); font-size: 15px; background-color: rgb(255, 255,
255);"><br>
</div>
<div style="line-height: 21.299999237060547px; color: rgb(68,
68, 68); font-size: 15px; background-color: rgb(255, 255,
255);">For frameshift variants I have to calculate downstream
effects and I have found this plugin made by your team. I have
a question that I would be very grateful if you could
address; </div>
<div style="line-height: 21.299999237060547px; color: rgb(68,
68, 68); font-size: 15px; background-color: rgb(255, 255,
255);"><span style="line-height: 22.719999313354492px;
font-size: 12pt;"><br>
</span></div>
<div style="line-height: 21.299999237060547px; color: rgb(68,
68, 68); font-size: 15px; background-color: rgb(255, 255,
255);"><span style="line-height: 22.719999313354492px;
font-size: 12pt;">As happens with other VEP plugins, I
suppose that downstream plugin is called from VEP command
line when the program is run. In case I have an annotated
output from a different program (i.e. snpEff) would it be
possible to adapt the plugin or run it separately of VEP?</span></div>
<div style="line-height: 21.299999237060547px; color: rgb(68,
68, 68); font-size: 15px; background-color: rgb(255, 255,
255);"><br>
</div>
<div style="line-height: 21.299999237060547px; color: rgb(68,
68, 68); font-size: 15px; background-color: rgb(255, 255,
255);">Thanks in advance for your time and patience,</div>
<br>
<div>
<hr id="stopSpelling">From: <a class="moz-txt-link-abbreviated" href="mailto:manueltar@hotmail.com">manueltar@hotmail.com</a><br>
To: <a class="moz-txt-link-abbreviated" href="mailto:dev@ensembl.org">dev@ensembl.org</a><br>
Subject: downstream.pm VEP plugin<br>
Date: Mon, 7 Jul 2014 13:33:57 +0200<br>
<br>
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<div dir="ltr"><span style="color:rgb(68, 68,
68);font-size:15px;line-height:21.299999237060547px;background-color:rgb(255,
255, 255);">Dear Mr Mclaren,</span>
<div style="line-height:21.299999237060547px;color:rgb(68,
68, 68);font-size:15px;background-color:rgb(255, 255,
255);"><br>
</div>
<div style="line-height:21.299999237060547px;color:rgb(68,
68, 68);font-size:15px;background-color:rgb(255, 255,
255);">My name is Manuel Tardaguila and I am an MSC in
bioinformatics doing a project in the university of
Lausanne. I am working on annotated variations using VEP
and snpEff as annotators.</div>
<div style="line-height:21.299999237060547px;color:rgb(68,
68, 68);font-size:15px;background-color:rgb(255, 255,
255);"><br>
</div>
<div style="line-height:21.299999237060547px;color:rgb(68,
68, 68);font-size:15px;background-color:rgb(255, 255,
255);">For frameshift variants I have to calculate
downstream effects and I have found this plugin made by
your team. I have a question that I would be very grateful
if you could address; </div>
<div style="line-height:21.299999237060547px;color:rgb(68,
68, 68);font-size:15px;background-color:rgb(255, 255,
255);"><span
style="line-height:22.719999313354492px;font-size:12pt;"><br>
</span></div>
<div style="line-height:21.299999237060547px;color:rgb(68,
68, 68);font-size:15px;background-color:rgb(255, 255,
255);"><span
style="line-height:22.719999313354492px;font-size:12pt;">As
happens with other VEP plugins, I suppose that
downstream plugin is called from VEP command line when
the program is run. In case I have an annotated output
from a different program (i.e. snpEff) would it be
possible to adapt the plugin or run it separately of
VEP?</span></div>
<div style="line-height:21.299999237060547px;color:rgb(68,
68, 68);font-size:15px;background-color:rgb(255, 255,
255);"><br>
</div>
<div style="line-height:21.299999237060547px;color:rgb(68,
68, 68);font-size:15px;background-color:rgb(255, 255,
255);">Thanks in advance for your time and patience,</div>
</div>
</div>
</div>
<br>
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<br>
<pre wrap="">_______________________________________________
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</pre>
</blockquote>
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