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<p>Hi David</p>
<p>VEP can run with 100K variants. The VEP publication (McLaren W et
al. 2016, doi:10.1186/s13059-016-0974-4) gives examples of<br>
number of variants and timings e.g for 4,474,140 variants.<br>
<br>
Were any warnings reported in your warnings_file ( --warning_file
/home/david/Desktop/tmp/tmp/vep_warnings.txt)?</p>
<p>From the stats file, there may be a problem with your input file
causing to to stop processing at Line 16856 of your input file.<br>
<br>
Regards<br>
Helen<br>
</p>
<div class="moz-cite-prefix">On 07/06/2019 10:17, David Tamborero
wrote:<br>
</div>
<blockquote type="cite"
cite="mid:CAMk_RaT_FWTDpSAw90h+9GnOttPdC9LjS4JDECM=NpggMRVqFQ@mail.gmail.com">
<meta http-equiv="content-type" content="text/html; charset=UTF-8">
<div dir="ltr">Hi all,
<div><br>
</div>
<div>I m working with VEP (command line) v95 to analyse (large)
vcf files and generate VEP -tab files</div>
<div><br>
</div>
<div>I ve realized that the output does not contain all the
entries that I m feeding to the tool. I ve been doing several
tests for vcf files with 1K, 5K, 10K, 20K, 50K, 100K entries
and it looks to me that VEP reads 'a maximum' of 16K8 variants
(see VEP stats output below)</div>
<div><br>
</div>
<div>I was not aware that it existed such a limit, nor I am
capable of finding any flag regarding this issue. I feel that
I m missing a big point, but I do not know which one --sorry
in advance if so.</div>
<div><br>
</div>
<div>command:</div>
<div>./vep -i blablabla.vcf -o blbabla.txt --tab --warning_file
blabla.txt --format vcf --cache --offline --force_overwrite
--hgvs --symbol --stats_file blablabla.txt --stats_text </div>
<div><br>
</div>
<div>version:</div>
<div>release 95<br>
sub 4f834538054c1aee24098c72f31f92d4c5aa303b<br>
</div>
<div><br>
</div>
<div>and the stats file content for the run with a vcf file with
100K entries :</div>
<div> [<font size="1">VEP run statistics]<br>
VEP version (API) 95 (95)<br>
Annotation sources Cache:
/home/david/.vep/homo_sapiens/95_GRCh37<br>
Species homo_sapiens<br>
Command line options --cache --dir /home/david/.vep
--force_overwrite --format vcf --hgvs --input_file
/home/david/Desktop/tmp/tmp/hq.vcf --offline --output_file
/home/david/Desktop/tmp/tmp/vep.txt --stats_file
/home/david/Desktop/tmp/tmp/stats_file.txt --stats_text
--symbol --tab --warning_file
/home/david/Desktop/tmp/tmp/vep_warnings.txt<br>
Start time 2019-06-07 10:50:24<br>
End time 2019-06-07 10:59:46<br>
Run time 562 seconds<br>
Input file /home/david/Desktop/tmp/tmp/hq.vcf<br>
Output file /home/david/Desktop/tmp/tmp/vep.txt<br>
<br>
[General statistics]<br>
<span style="background-color:rgb(255,217,102)">Lines of
input read 16856</span><br>
Variants processed 16855<br>
Variants filtered out 0<br>
Novel / existing variants -<br>
Overlapped genes 2809<br>
Overlapped transcripts 15672<br>
Overlapped regulatory features -</font></div>
</div>
<br>
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