<!DOCTYPE html>
<html>
<head>
<meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
</head>
<body>
<p>Hi Ivan,</p>
<p>Sorry to hear that the functionality is not as expected. I am
able to replicate the issue with the input and we will try to
provide a fix in the coming release.</p>
<p>Kind regards,</p>
<p>Likhitha<br>
</p>
<div class="moz-cite-prefix">On 07/08/2024 21:52, Adzhubey, Ivan A.
wrote:<br>
</div>
<blockquote type="cite"
cite="mid:162486a7-6490-4fbb-a617-b972eec78389@hms.harvard.edu">
<meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
<p>Hi,</p>
<p>VEP command line v112, run on Linux:<br>
</p>
<p>Looks like, despite what the documentation says,
UPLOADED_ALLELE field is always output minimized in case of
indels, rendering it useless. See the full test input and VEP
output files attached.</p>
<p><span style="font-family:monospace"><span
style="color:#000000;background-color:#ffffff;"># input file<br>
$ cat test.vcf </span><br>
##fileformat=VCFv4.2 <br>
##source=test <br>
##reference=GRCh38 <br>
#CHROM POS ID REF ALT QUAL FILTER INFO <br>
1 961320 1:961320:G/GCAGGCTCGGCC G GCAGGCTCGGCC
. PASS .<br>
</span></p>
<p><span style="font-family:monospace"><span
style="color:#000000;background-color:#ffffff;"># the
</span></span><span style="font-family:monospace">UPLOADED_ALLELE
field contents </span>
<span style="font-family:monospace"><span
style="color:#000000;background-color:#ffffff;">in output is
definitely NOT the uploaded allele<br>
$ grep -v '^##' test.vep.tsv | cut -f15 </span><br>
UPLOADED_ALLELE <br>
-/CAGGCTCGGCC<br>
</span></p>
<p><span style="font-family:monospace">Best,</span></p>
<p><span style="font-family:monospace">Ivan<br>
</span></p>
<pre class="moz-signature"
signature-switch-id="a087f893-50f9-4ebb-9789-891c9951f2f9"
cols="72">--
Ivan Adzhubey, Ph.D.
Research Associate
Department of Biomedical Informatics
Harvard Medical School
10 Shattuck Street, Suite 514
Boston, MA 02115
tel: (617) 432-2144
fax: (617) 432-0693
web: <a class="moz-txt-link-freetext"
href="https://sunyaevlab.hms.harvard.edu/wiki/!web/start"
moz-do-not-send="true">https://sunyaevlab.hms.harvard.edu/wiki/!web/start</a></pre>
<br>
<fieldset class="moz-mime-attachment-header"></fieldset>
<pre class="moz-quote-pre" wrap="">_______________________________________________
Dev mailing list <a class="moz-txt-link-abbreviated" href="mailto:Dev@ensembl.org">Dev@ensembl.org</a>
Posting guidelines and subscribe/unsubscribe info: <a class="moz-txt-link-freetext" href="https://lists.ensembl.org/mailman/listinfo/dev_ensembl.org">https://lists.ensembl.org/mailman/listinfo/dev_ensembl.org</a>
Ensembl Blog: <a class="moz-txt-link-freetext" href="http://www.ensembl.info/">http://www.ensembl.info/</a>
</pre>
</blockquote>
</body>
</html>