<div dir="ltr">Hi Guillermo,<div><br>I'm unable to recreate this, sorry!</div><div><br></div><div style>I get 406 going in, 406 coming out every time, whichever combination of those options above I use, and whether I use VCF or standard output.</div>
<div style><br></div><div style>Here's my run (minus -check_sv):</div><div style><br></div><div style><div>> perl <a href="http://variant_effect_predictor.pl">variant_effect_predictor.pl</a> -i guill.vcf -vcf -cache -force -fork 4 -hgvs -canon -ccds -domains -gmaf -hgnc -maf_1kg -numbers -poly b -regu -sift b -fasta ~/NFS/Fasta/Homo_sapiens.GRCh37.69.dna.primary_assembly.fa</div>
<div>2013-05-21 13:24:26 - Checking/creating FASTA index</div><div>2013-05-21 13:24:26 - Read existing cache info</div><div>2013-05-21 13:24:26 - Starting...</div><div>2013-05-21 13:24:26 - Detected format of input file as vcf</div>
<div>2013-05-21 13:24:26 - Read 406 variants into buffer</div><div>2013-05-21 13:24:26 - Reading transcript data from cache and/or database</div><div>[================================================================] [ 100% ]</div>
<div>2013-05-21 13:24:30 - Retrieved 10891 transcripts (0 mem, 10919 cached, 0 DB, 28 duplicates)</div><div>2013-05-21 13:24:30 - Reading regulatory data from cache and/or database</div><div>[================================================================] [ 100% ]</div>
<div>2013-05-21 13:24:35 - Retrieved 36955 regulatory features (0 mem, 36955 cached, 0 DB, 0 duplicates)</div><div>2013-05-21 13:24:35 - Calculating consequences</div><div>[================================================================] [ 100% ]</div>
<div>2013-05-21 13:24:56 - Writing output2013-05-21 13:24:56 - Processed 406 total variants (14 vars/sec, 14 vars/sec total)</div><div>2013-05-21 13:24:56 - Wrote stats summary to variant_effect_output.txt_summary.html</div>
<div>2013-05-21 13:24:56 - Finished!</div><div style>> wc -l variant_effect_output.txt</div><div style>408</div><div style><br></div><div style>It's 408 as it's adding two header lines to the VCF output.</div><div style>
<br></div><div style>Which 16 are missing from your output, and is it the same 16 each time?</div><div style><br></div><div style>Try writing to a different output file, or on a different disk if you can (perhaps disk space is an issue?)</div>
<div style><br></div><div style>Will</div></div></div><div class="gmail_extra"><br><br><div class="gmail_quote">On 21 May 2013 13:15, 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">
<div>Hello Will,<br>
<br>
Here's the input:
<a href="https://github.com/guillermomarco/vep_plugins_71/blob/master/missing_variants/missing_output_variants.vcf" target="_blank">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.<div><div class="h5"><br>
<br>
<br>
On 05/21/2013 01:49 PM, Will McLaren wrote:<br>
</div></div></div><div><div class="h5">
<blockquote type="cite">
<div dir="ltr">Hi Guillermo,
<div><br>
</div>
<div>None of those options should filter out variants.</div>
<div><br>
</div>
<div>Are you able to provide any of the files that
recreate the problem?</div>
<div>
<br>
</div>
<div>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><br>
</div>
<div>Regards</div>
<div><br>
</div>
<div>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>
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</div>
</blockquote>
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