<html><head><meta http-equiv="Content-Type" content="text/html charset=us-ascii"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class="">Hi Will, Ensembl/VEP folk,<div class=""><br class=""></div><div class="">I'm getting a weird multi-allelic issue in VEP v81 - when I annotate the below VCF, all annotations for the first site get an ALLELE_NUM of 2, which results in G->C being annotated as a frameshift (works fine when the SNV is on its own). Any ideas why this might be happening?<br class=""><div class="">
<div style="color: rgb(0, 0, 0); letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px; word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class=""><div style="color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px;" class=""><br class="Apple-interchange-newline">-Konrad</div></div>
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<br class=""><div class=""><div class="">##fileformat=VCFv4.1</div><div class="">#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT</div><div class="">1<span class="Apple-tab-span" style="white-space:pre"> </span>898175<span class="Apple-tab-span" style="white-space:pre"> </span>.<span class="Apple-tab-span" style="white-space:pre"> </span>G<span class="Apple-tab-span" style="white-space:pre"> </span>GC,C<span class="Apple-tab-span" style="white-space:pre"> </span>.<span class="Apple-tab-span" style="white-space:pre"> </span>.<span class="Apple-tab-span" style="white-space:pre"> </span>.<span class="Apple-tab-span" style="white-space:pre"> </span>.</div><div class="">1<span class="Apple-tab-span" style="white-space:pre"> </span>898175<span class="Apple-tab-span" style="white-space:pre"> </span>.<span class="Apple-tab-span" style="white-space:pre"> </span>G<span class="Apple-tab-span" style="white-space:pre"> </span>C<span class="Apple-tab-span" style="white-space:pre"> </span>.<span class="Apple-tab-span" style="white-space:pre"> </span>.<span class="Apple-tab-span" style="white-space:pre"> </span>.<span class="Apple-tab-span" style="white-space:pre"> </span>.</div></div></div></body></html>