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<div class="moz-cite-prefix">Hello Will,<br>
<br>
I'm getting more 3000 lines of file output.. this seems really
weird....<br>
<br>
<pre>wc -l variant_effect_output.txt</pre>
<b>3936</b><br>
<br>
Here's the way I'm proceeding:<br>
<br>
<pre>./variant_effect_predictor.pl -i /home/likewise-open/SGNET/gmarco/vep_71_annotation_check/input.vcf -force -fork 4 --database --config vep_71.test</pre>
<br>
Here's the content of vep_71.test:<br>
<br>
dir /home/likewise-open/SGNET/gmarco/.vep<br>
toplevel_dir /home/likewise-open/SGNET/gmarco/.vep<br>
force_overwrite 1<br>
format vcf<br>
html 1<br>
host 192.19.x.xx<br>
port 3306<br>
user myuser<br>
password mypassword<br>
buffer_size 5000<br>
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<br>
<br>
Best regards,<br>
Guillermo.<br>
<br>
On 05/21/2013 02:30 PM, Will McLaren wrote:<br>
</div>
<blockquote
cite="mid:CAMVEDX1uqoMqwE=kZU=VH8iU8fRfyN3Y=32TB4AqcPeGJyjApA@mail.gmail.com"
type="cite">
<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 moz-do-not-send="true"
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 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">
<div>Hello Will,<br>
<br>
Here's the input: <a moz-do-not-send="true"
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
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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