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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>
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