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<div class="moz-cite-prefix">Hello,<br>
<br>
I'm looking for an example *.vcf output with ALL the "Extra"
parameters.<br>
I've generated some with VEP script but i'm missing some extras
never being generated like HGNC.<br>
<br>
A few lines VCF with all values would be enough, since i'm
planning to parse "Extra" column.<br>
<br>
It also would be great if it includes most of the plugins outputs
also :)<br>
<br>
Thank you :)<br>
<br>
Best regards,<br>
Guillermo.<br>
<br>
On 04/16/13 18:00, Guillermo Marco Puche wrote:<br>
</div>
<blockquote cite="mid:516D7597.1030409@sistemasgenomicos.com"
type="cite">
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<div class="moz-cite-prefix">On 04/16/13 14:49, Will McLaren
wrote:<br>
</div>
<blockquote
cite="mid:CAMVEDX26j5aBgFzy_n5pg1qpUYHpwvqgyG05L3rrOX3LUg-W-g@mail.gmail.com"
type="cite">
<pre wrap="">Hi Guillermo,
There's two distinct ways you can add additional data to the output
from the VEP.
1) Custom annotations - here you simply provide the VEP with a
tabix-indexed position-based data file, and the VEP does the work of
finding overlaps with your variant input and the data from the file.
2) Plugins - you write the code to add to or manipulate the internal
data structures used by the VEP. In its simplest form, a plugin can be
simply looking up an attribute of some object and adding it to the
output.
Writing a plugin requires a basic understanding of the Ensembl API,
but getting a basic plugin working requires only a very small amount
of code.
</pre>
</blockquote>
Since additional data is being obtained from multiple sources,
APIs, files, etc.. I guess plugins are the only way to go for me.<br>
<blockquote
cite="mid:CAMVEDX26j5aBgFzy_n5pg1qpUYHpwvqgyG05L3rrOX3LUg-W-g@mail.gmail.com"
type="cite">
<pre wrap="">The documentation
(<a moz-do-not-send="true" class="moz-txt-link-freetext" href="http://www.ensembl.org/info/docs/variation/vep/vep_script.html#plugins">http://www.ensembl.org/info/docs/variation/vep/vep_script.html#plugins</a>)
explains all of this, but the best way to see how plugins work is to
look at the existing plugins at
<a moz-do-not-send="true" class="moz-txt-link-freetext" href="https://github.com/ensembl-variation/VEP_plugins">https://github.com/ensembl-variation/VEP_plugins</a>. I'd suggest looking
at Conservation.pm and ProteinSeqs.pm as some relatively simple
examples of retrieving additional data from the API.
</pre>
</blockquote>
Where are packages like<span class="nb" style="margin: 0px;
padding: 0px; border: 0px; color: rgb(0, 134, 179);"> package</span>
<span class="n" style="margin: 0px; padding: 0px; border: 0px;
color: rgb(51, 51, 51);">Conservation</span><span class="p"
style="margin: 0px; padding: 0px; border: 0px;">; comming from?<br>
</span>
<blockquote
cite="mid:CAMVEDX26j5aBgFzy_n5pg1qpUYHpwvqgyG05L3rrOX3LUg-W-g@mail.gmail.com"
type="cite">
<pre wrap="">You should note that using VCF output you will see repeated elements
in the INFO field added, since the plugin gets run once for every
variant/transcript overlap; all data appear under the CSQ field in the
INFO column. Currently there is no way for the VEP via plugins to add
separate INFO fields, however this is something we are looking into,
and in fact would be relatively easy to "hack" in for someone
determined enough (see subroutine vf_list_to_cons in
Bio::EnsEMBL::Variation::Utils::VEP).
</pre>
</blockquote>
I'll look further into this tomorrow since I've to go now.<br>
<br>
A workaround could be simply generating a temp file with extra
columns and in the end merge original VCF from VEP script with the
output from plugins for additional columns.<br>
<br>
Maybe I missunderstood you. Correct me if i'm wrong please.<br>
<blockquote
cite="mid:CAMVEDX26j5aBgFzy_n5pg1qpUYHpwvqgyG05L3rrOX3LUg-W-g@mail.gmail.com"
type="cite">
<pre wrap="">Hope this helps, and feel free to ask further questions!
Will McLaren
Ensembl Variation</pre>
</blockquote>
Thank you so much.<br>
<br>
Best regards,<br>
Guillermo.<br>
<blockquote
cite="mid:CAMVEDX26j5aBgFzy_n5pg1qpUYHpwvqgyG05L3rrOX3LUg-W-g@mail.gmail.com"
type="cite">
<pre wrap="">
On 16 April 2013 12:58, Guillermo Marco Puche
<a moz-do-not-send="true" class="moz-txt-link-rfc2396E" href="mailto:guillermo.marco@sistemasgenomicos.com"><guillermo.marco@sistemasgenomicos.com></a> wrote:
</pre>
<blockquote type="cite">
<pre wrap="">Hello,
I'm in need to develop some extra features for VEP.
My input files are in VCF format and also my output.
But I want to add several additional columns for extra data at the VCF out.
For example,AA conservation score, Biobase description, Biobase link, MAF
populations, Flanking sequence, Gene description, InterPro_ID and more..
I've been reading the documents and I'm a bit confused about "Custom
annotations".
I think since the data I want is extra on the output and not in the input,
what I should do is develop several Plugins to obtain all the values I need.
I think most of them can be obtained through the Ensembl API even if I'm new
to this. Other will require more hard coding.
I hope someone can clarify me a bit on this matter.
Thank you.
Best regards,
Guillermo.
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<br>
<br>
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