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<p>Hi, Will,</p>
<p>Yes, thank you--that works perfectly. I just had to upgrade to
v87 (was on v84, where this option apparently didn't exist).</p>
<p>regards</p>
<p>Afif<br>
</p>
<pre class="moz-signature" cols="72">Afif Elghraoui
Laboratory for Pathogenesis of Clinical Drug Resistance and Persistence
San Diego State University
Alvarado Medical Center
6367 Alvarado Court, Suite 206
San Diego, CA 92120
p. 858-222-0454
<a class="moz-txt-link-freetext" href="http://tuberculosis.sdsu.edu">http://tuberculosis.sdsu.edu</a></pre>
<div class="moz-cite-prefix">On 02/06/2017 03:26 AM, Will McLaren
wrote:<br>
</div>
<blockquote
cite="mid:CAMVEDX0u6TjuSgAUxh=OCfDc558U-hpbZeUDrTvCbw+hpofBcQ@mail.gmail.com"
type="cite">
<div dir="ltr">Hi Afif,
<div><br>
</div>
<div>You may provide a tab-delimited chromosome synonyms file to
VEP that maps (in either direction) the names of your
chromosomes as input to the names of the chromosomes as found
in the VEP cache. Here we create a simple one as you only
require mapping between one chromosome name set!</div>
<div><font face="monospace, monospace"><br>
</font></div>
<div><font face="monospace, monospace">$ echo "Chromosome\t1"
> chr_synonyms.txt</font></div>
<div><font face="monospace, monospace">$ [vep_command]
--synonyms chr_synonyms.txt</font></div>
<div><br>
</div>
<div>Hope that helps</div>
<div><br>
</div>
<div>Will McLaren</div>
<div>Ensembl Variation</div>
<div><br>
</div>
</div>
<div class="gmail_extra"></div>
<br>
</blockquote>
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