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<div class="moz-cite-prefix">Hello,<br>
<br>
Ok this seems to clarify all.<br>
<br>
What about plugins with also variant_feature_types sub-routine?<br>
<br>
sub variant_feature_types {<br>
return ['VariationFeature'];<br>
}<br>
<br>
Thank you.<br>
<br>
Best regards,<br>
Guillermo.<br>
<br>
On 05/09/2013 10:19 AM, Will McLaren wrote:<br>
</div>
<blockquote
cite="mid:CAMVEDX2hJ_SH9-CaRbn4h78a59_x9FLWTpcKJ6b4Fq7rH3DCZg@mail.gmail.com"
type="cite">
<div dir="ltr">Hi Guillermo,
<div><br>
</div>
<div style="">The feature_types sub determines when the plugin
is run depending on what feature type the
TranscriptVariationAllele object overlaps.</div>
<div style=""><br>
</div>
<div style="">
To enable your plugin to run on every variant, regardless of
what it overlaps, you should have the sub return:</div>
<div style=""><br>
</div>
<div style="">return ['Feature','Intergenic'];</div>
<div style=""><br>
</div>
<div style="">Remove 'Intergenic' if you don't want the plugin
to run on variants that don't overlap a transcript or
regulatory feature.</div>
<div style=""><br>
</div>
<div style="">'Feature' is a catch-all type that includes
transcripts and regulatory feature types.</div>
<div style=""><br>
</div>
<div style="">Hope this helps</div>
<div style=""><br>
</div>
<div style="">Will</div>
</div>
<div class="gmail_extra"><br>
<br>
<div class="gmail_quote">On 9 May 2013 08:11, 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"> Hello,<br>
<br>
While I'm using VEP flag "--regulatory" flag I notice a
weird output in my vep file.<br>
Some lines present all empty columns except: Consequence,
Feature and Feature_type.<br>
<br>
While I'm using VEP plugin Conservation (available in VEP
github repository) some lines present all empty columns
except: Consequence, Feature, Feature_type and
Conservation.<br>
<br>
I would like that the rest of my columns (obtained from
VCF through plugin) are also show. I think this has
something to do with the following lines in my plugin:<br>
<br>
<pre>sub feature_types {</pre>
<pre> return ['Transcript'];</pre>
<pre>}
</pre>
I'm am wrong?<br>
<br>
Thank you !<br>
<br>
Best regards,<br>
Guillermo.<br>
</div>
<br>
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