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<div class="moz-cite-prefix">Hello Will,<br>
<br>
You was right. I'm getting the 406 variants.<br>
I just dropped html in case.<br>
<br>
As always flawless Ensembl support. Thank you !<br>
<br>
Best regards,<br>
Guillermo.<br>
<br>
On 05/21/2013 05:13 PM, Will McLaren wrote:<br>
</div>
<blockquote
cite="mid:CAMVEDX2UJPCnZqVOOONaRpRNKQ-dt8UeHVGY2zDrKDWDOarDeQ@mail.gmail.com"
type="cite">
<div dir="ltr">You get one line of output for each variant/feature
overlap, so you will almost always see more output lines than
input if you use the default output format. If you use VCF
output, you only get one line per variant.
<div>
<br>
</div>
<div>You can check how many unique variants there are in the
output with e.g.:</div>
<div><br>
</div>
<div>grep -v # variant_effect_output.txt | cut -f 1 | sort -u |
wc -l<br>
</div>
<div><br>
</div>
<div style="">assuming your variants have unique names.</div>
<div><br>
</div>
<div style="">Try dropping "html" from your config, see if that
makes any difference - as the newest feature there, it's got a
higher chance of causing problems!</div>
<div style=""><br>
</div>
<div style="">
Will</div>
<div><br>
</div>
<div><br>
</div>
</div>
<div class="gmail_extra"><br>
<br>
<div class="gmail_quote">On 21 May 2013 16:02, 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>
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>./<a moz-do-not-send="true" href="http://variant_effect_predictor.pl" target="_blank">variant_effect_predictor.pl</a> -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
<div class="im"><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>
</div>
Best regards,<br>
Guillermo.
<div>
<div class="h5"><br>
<br>
On 05/21/2013 02:30 PM, Will McLaren wrote:<br>
</div>
</div>
</div>
<div>
<div class="h5">
<blockquote type="cite">
<div dir="ltr">Hi Guillermo,
<div><br>
I'm unable to recreate this, sorry!</div>
<div><br>
</div>
<div>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><br>
</div>
<div>Here's my run (minus -check_sv):</div>
<div><br>
</div>
<div>
<div>> perl <a moz-do-not-send="true"
href="http://variant_effect_predictor.pl"
target="_blank">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>> wc -l variant_effect_output.txt</div>
<div>408</div>
<div><br>
</div>
<div>It's 408 as it's adding two header lines to
the VCF output.</div>
<div> <br>
</div>
<div>Which 16 are missing from your output, and
is it the same 16 each time?</div>
<div><br>
</div>
<div>Try writing to a different output file, or
on a different disk if you can (perhaps disk
space is an issue?)</div>
<div><br>
</div>
<div>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><br>
<br>
<br>
On 05/21/2013 01:49 PM, Will McLaren
wrote:<br>
</div>
</div>
</div>
<div>
<div>
<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>
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