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<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">https://sunyaevlab.hms.harvard.edu/wiki/!web/start</a></pre>
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