<div dir="ltr">Hello,<div><br></div><div style>Some variants are parsed by the VEP as structural variants, and these are treated subtly differently as typically they are much larger than regular sequence variants.</div><div style>
<br></div><div style>To enable your plugin to process both types, you should use:</div><div style><br></div><div style>return ['BaseVariationFeature'];</div><div style><br></div><div style>or for just structural variants</div>
<div style><br></div><div style>return ['StructuralVariationFeature'];</div><div style><br></div><div style>Regards</div><div style><br></div><div style>Will</div></div><div class="gmail_extra"><br><br><div class="gmail_quote">
On 9 May 2013 10:33, Guillermo Marco Puche <span dir="ltr"><<a 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">
<div>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.<div><div class="h5"><br>
<br>
On 05/09/2013 10:19 AM, Will McLaren wrote:<br>
</div></div></div><div><div class="h5">
<blockquote type="cite">
<div dir="ltr">Hi Guillermo,
<div><br>
</div>
<div>The feature_types sub determines when the plugin
is run depending on what feature type the
TranscriptVariationAllele object overlaps.</div>
<div><br>
</div>
<div>
To enable your plugin to run on every variant, regardless of
what it overlaps, you should have the sub return:</div>
<div><br>
</div>
<div>return ['Feature','Intergenic'];</div>
<div><br>
</div>
<div>Remove 'Intergenic' if you don't want the plugin
to run on variants that don't overlap a transcript or
regulatory feature.</div>
<div><br>
</div>
<div>'Feature' is a catch-all type that includes
transcripts and regulatory feature types.</div>
<div><br>
</div>
<div>Hope this helps</div>
<div><br>
</div>
<div>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 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>
_______________________________________________<br>
Dev mailing list <a href="mailto:Dev@ensembl.org" target="_blank">Dev@ensembl.org</a><br>
Posting guidelines and subscribe/unsubscribe info: <a href="http://lists.ensembl.org/mailman/listinfo/dev" target="_blank">http://lists.ensembl.org/mailman/listinfo/dev</a><br>
Ensembl Blog: <a href="http://www.ensembl.info/" target="_blank">http://www.ensembl.info/</a><br>
<br>
</blockquote>
</div>
<br>
</div>
<br>
<fieldset></fieldset>
<br>
<pre>_______________________________________________
Dev mailing list <a href="mailto:Dev@ensembl.org" target="_blank">Dev@ensembl.org</a>
Posting guidelines and subscribe/unsubscribe info: <a href="http://lists.ensembl.org/mailman/listinfo/dev" target="_blank">http://lists.ensembl.org/mailman/listinfo/dev</a>
Ensembl Blog: <a href="http://www.ensembl.info/" target="_blank">http://www.ensembl.info/</a>
</pre>
</blockquote>
</div></div></div>
<br>_______________________________________________<br>
Dev mailing list <a href="mailto:Dev@ensembl.org">Dev@ensembl.org</a><br>
Posting guidelines and subscribe/unsubscribe info: <a href="http://lists.ensembl.org/mailman/listinfo/dev" target="_blank">http://lists.ensembl.org/mailman/listinfo/dev</a><br>
Ensembl Blog: <a href="http://www.ensembl.info/" target="_blank">http://www.ensembl.info/</a><br>
<br></blockquote></div><br></div>