<div dir="ltr">Hi Nicolas,<div><br>Thanks for the report - some of the headers were getting scrambled internally.</div><div><br></div><div>I've pushed fixes to release/81 of ensembl-tools (the <a href="http://variant_effect_predictor.pl">variant_effect_predictor.pl</a> script) and the ExAC.pm plugin file - please re-download VEP and re-run the installer.</div><div><br></div><div>Regards</div><div><br></div><div>Will McLaren</div><div>Ensembl Variation</div></div><div class="gmail_extra"><br><div class="gmail_quote">On 5 August 2015 at 17:24, Nicolas Thierry-Mieg <span dir="ltr"><<a href="mailto:Nicolas.Thierry-Mieg@imag.fr" target="_blank">Nicolas.Thierry-Mieg@imag.fr</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">Hi all,<br>
<br>
I'm experimenting with the ExAC plugin for VEP. I've noticed that I only obtain the global ExAC_AF but not the population-specific ExAC_*_AF values when using the --vcf option. Withouth this option it works.<br>
Details follow.<br>
<br>
<br>
For these tests I DL'd the latest VEP v81 available today, used INSTALL.pl, installed homo_sapiens_refseq_vep_81_GRCh37.tar.gz as a cache as well as the ExAC.pm plugin (both via INSTALL.pl). And I DL'd ExAC.r0.3.sites.vep.vcf.gz from the broad ftp.<br>
<br>
$ more input.vcf<br>
#CHROM POS ID REF ALT QUAL FILTER INFO<br>
chr1 26131654 . G A 67.09 PASS <br>
<br>
$ <a href="http://variant_effect_predictor.pl" rel="noreferrer" target="_blank">variant_effect_predictor.pl</a> -i input.vcf -o ttt.vcf --vcf --offline --refseq --plugin ExAC,/home/nthierry/Software/ExAC/ExAC.r0.3.sites.vep.vcf.gz --force<br>
2015-08-05 17:34:41 - Read existing cache info<br>
2015-08-05 17:34:41 - Loaded plugin: ExAC<br>
2015-08-05 17:34:41 - Starting...<br>
2015-08-05 17:34:41 - Detected format of input file as vcf<br>
2015-08-05 17:34:41 - Read 1 variants into buffer<br>
2015-08-05 17:34:41 - Reading transcript data from cache and/or database<br>
[===============================================] [ 100% ]<br>
2015-08-05 17:34:41 - Retrieved 92 transcripts (0 mem, 236 cached, 0 DB, 0 duplicates)<br>
2015-08-05 17:34:41 - Analyzing chromosome 1<br>
2015-08-05 17:34:41 - Analyzing variants<br>
[===============================================] [ 100% ]<br>
2015-08-05 17:34:41 - Calculating consequences<br>
2015-08-05 17:34:41 - Processed 1 total variants (1 vars/sec, 1 vars/sec total)<br>
2015-08-05 17:34:41 - Wrote stats summary to ttt.vcf_summary.html<br>
2015-08-05 17:34:41 - Finished!<br>
<br>
<br>
So, it seems to run OK, but the produced ttt.vcf ends with |||||0.814||| . I would expect these (empty) fields to contain values.<br>
<br>
<br>
If I remove --vcf from my command, the output vcf contains population-specific allele freqs, as expected, eg:<br>
ExAC_AF_FIN=0.728;IMPACT=MODERATE;ExAC_AF=0.814;ExAC_AF_OTH=0.816;[...]<br>
<br>
As a side note, as you can see without --vcf the fields are called ExAC_AF_* , but in the same file they are documented as ExAC_*_AF, eg:<br>
## ExAC_EAS_AF : ExAC East Asian Allele frequency<br>
This last point is just a minor glitch, but you may want to fix it as well.<br>
<br>
<br>
Regards,<br>
Nicolas<br>
<br>
<br>
-- <br>
-----------------------------------------------------------<br>
Nicolas Thierry-Mieg<br>
Laboratoire TIMC-IMAG/BCM, CNRS UMR 5525<br>
Pavillon Taillefer, Faculte de Medecine<br>
38700 La Tronche, France<br>
tel: <a href="tel:%28%2B33%29456.520.067" value="+33456520067" target="_blank">(+33)456.520.067</a>, fax: <a href="tel:%28%2B33%29456.520.055" value="+33456520055" target="_blank">(+33)456.520.055</a><br>
------------------------------------------------------------<br>
<br>
_______________________________________________<br>
Dev mailing list <a href="mailto:Dev@ensembl.org" target="_blank">Dev@ensembl.org</a><br>
Posting guidelines and subscribe/unsubscribe info: <a href="http://lists.ensembl.org/mailman/listinfo/dev" rel="noreferrer" target="_blank">http://lists.ensembl.org/mailman/listinfo/dev</a><br>
Ensembl Blog: <a href="http://www.ensembl.info/" rel="noreferrer" target="_blank">http://www.ensembl.info/</a><br>
</blockquote></div><br></div>