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<div class="moz-cite-prefix">Hello Will,<br>
<br>
Here's the input:
<meta http-equiv="content-type" content="text/html;
charset=ISO-8859-1">
<a
href="https://github.com/guillermomarco/vep_plugins_71/blob/master/missing_variants/missing_output_variants.vcf">https://github.com/guillermomarco/vep_plugins_71/blob/master/missing_variants/missing_output_variants.vcf</a><br>
<br>
As you said it's not about the options or plugins. Launching VEP
without specyfiying any option still returns an output with
missing variants.<br>
<br>
Regards,<br>
Guillermo.<br>
<br>
<br>
On 05/21/2013 01:49 PM, Will McLaren wrote:<br>
</div>
<blockquote
cite="mid:CAMVEDX0ugZXmdRXJ6gXciq9hMaZY0E=1dNkyA4tsUg6oa+yyeg@mail.gmail.com"
type="cite">
<div dir="ltr">Hi Guillermo,
<div><br>
</div>
<div style="">None of those options should filter out variants.</div>
<div style=""><br>
</div>
<div style="">Are you able to provide any of the files that
recreate the problem?</div>
<div style="">
<br>
</div>
<div style="">Is there any chance that you are using VCF input
and it contains non-variant lines - this would be where the
ALT column is empty or "."? If so, this may be your problem.
To force these to be included in the output, you should add
--allow_non_variant.</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 21 May 2013 09:40, 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>
I've been checking VEP results, and i've noticed that I'm
missing some input variants in the output.<br>
<br>
I think this may be issued to some of the options i'm
using to launch vep:<br>
<br>
<small><small>hgvs 1<br>
canonical 1<br>
ccds 1<br>
check_svs 1<br>
domains 1<br>
gmaf 1<br>
hgnc 1<br>
maf_1kg 1<br>
numbers 1<br>
polyphen b<br>
regulatory 1<br>
sift b</small></small><br>
<br>
Should be any of these options filtering output? I've
disabled all plugins to run this test to be sure that it's
not a plugin issue.<br>
<br>
<ul>
<li>With a 406 variant input vcf file, I've missed 16
variants. <br>
</li>
<li>I then ran VEP with only those 16 missing variants
and missed 3 on output. <br>
</li>
<li>Rerun again and now with 3 missing variants and now
not a single one was missing.</li>
</ul>
<p>I would like to know what's behind that weird
behaviour.<br>
</p>
<p>Thank you.<br>
</p>
<p>Best regards,<br>
Guillermo.<br>
</p>
<br>
<br>
</div>
<br>
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</blockquote>
</div>
</div>
</blockquote>
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