<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 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>_______________________________________________<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>