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<div class="moz-cite-prefix">Hi Will,<br>
<br>
The former, and thanks!<br>
<br>
Cheers<br>
<br>
Stuart<br>
<br>
On 14/05/2013 09:35, Will McLaren wrote:<br>
</div>
<blockquote
cite="mid:CAMVEDX3D5CVq9jT3sU5YGvSBZOcna+1JR_H6eAvF7pGT4sdzQw@mail.gmail.com"
type="cite">
<div dir="ltr">Hi Stuart,
<div><br>
</div>
<div>I'm not sure what you mean - do you want the reference
allele in a column on each row? Or do you want to consider the
reference allele as an alternate allele?</div>
<div><br>
</div>
<div style="">For the former, you'd have to write a plugin,
something like:</div>
<div style=""><br>
</div>
<div style="">
<div>package RefAllele;</div>
<div><br>
</div>
<div>use strict;</div>
<div>use warnings;</div>
<div><br>
</div>
<div>use base
qw(Bio::EnsEMBL::Variation::Utils::BaseVepPlugin);</div>
<div><br>
</div>
<div>sub feature_types {</div>
<div> return ['Feature','Intergenic'];</div>
<div>}</div>
<div><br>
</div>
<div>sub get_header_info {</div>
<div> return {</div>
<div> RefAllele => "Reference allele",</div>
<div> };</div>
<div>}</div>
<div><br>
</div>
<div style="">sub run {</div>
<div style=""> my ($self, $tva) = @_;</div>
<div style=""> return { RefAllele => (split "/",
$tva->variation_feature->allele_string)[0] };</div>
<div style="">}</div>
<div style=""><br>
</div>
<div style="">For the latter, I don't think it can be done,
and wouldn't make much sense!</div>
<div style=""><br>
</div>
<div style="">Regards</div>
<div style=""><br>
</div>
<div style="">Will</div>
</div>
</div>
<div class="gmail_extra"><br>
<br>
<div class="gmail_quote">On 14 May 2013 08:35, Stuart Meacham <span
dir="ltr"><<a moz-do-not-send="true"
href="mailto:sm766@cam.ac.uk" target="_blank">sm766@cam.ac.uk</a>></span>
wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0
.8ex;border-left:1px #ccc solid;padding-left:1ex">
Hi,<br>
<br>
Simple question: what is the easiest way to get the
reference allele from a vcf formatted input file into a
'default' formatted output file whilst using the latest
version of the Variant Effect Predictor?<br>
<br>
Thanks<br>
<br>
Stuart<br>
<br>
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</blockquote>
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