<div dir="ltr">Hi Konrad,<div><br></div><div>The --minimal flag is resolving both ALTs to "C", so the code I had in place which was a hash indexed on the resolved allele won't work in this case.</div><div><br></div><div>I've had to refactor the code for how the allele number is determined, so I'm reluctant to push this fix to a release branch.</div><div><br></div><div>It is on master, however, and should you wish to grab the fix for your checkout, you could cherry-pick the commit to your ensembl-variation git checkout:</div><div><br></div><div>cd ~/src/ensembl-variation</div><div>git fetch</div><div>git cherry-pick 0013c9e</div><div><br></div><div>Or if you don't want to go the cherry pick way, you'll need to replace the following files with those from master:</div><div><br></div><div>modules/Bio/EnsEMBL/Variation/Utils/VEP.pm</div><div>modules/Bio/EnsEMBL/Variation/VariationFeatureOverlap.pm</div><div>modules/Bio/EnsEMBL/Variation/VariationFeatureOverlapAllele.pm</div><div><br></div><div>Thanks again for the bug reports</div><div><br></div><div>Will</div></div><div class="gmail_extra"><br><div class="gmail_quote">On 22 August 2015 at 17:22, Konrad Karczewski <span dir="ltr"><<a href="mailto:konradk@broadinstitute.org" target="_blank">konradk@broadinstitute.org</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div style="word-wrap:break-word">Hi Will, Ensembl/VEP folk,<div><br></div><div>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><div>
<div style="color:rgb(0,0,0);letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;word-wrap:break-word"><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;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px"><br>-Konrad</div></div>
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<br><div><div>##fileformat=VCFv4.1</div><div>#CHROM  POS     ID      REF     ALT     QUAL    FILTER  INFO    FORMAT</div><div>1<span style="white-space:pre-wrap">     </span>898175<span style="white-space:pre-wrap">  </span>.<span style="white-space:pre-wrap">       </span>G<span style="white-space:pre-wrap">       </span>GC,C<span style="white-space:pre-wrap">    </span>.<span style="white-space:pre-wrap">       </span>.<span style="white-space:pre-wrap">       </span>.<span style="white-space:pre-wrap">       </span>.</div><div>1<span style="white-space:pre-wrap">       </span>898175<span style="white-space:pre-wrap">  </span>.<span style="white-space:pre-wrap">       </span>G<span style="white-space:pre-wrap">       </span>C<span style="white-space:pre-wrap">       </span>.<span style="white-space:pre-wrap">       </span>.<span style="white-space:pre-wrap">       </span>.<span style="white-space:pre-wrap">       </span>.</div></div></div></div><br>_______________________________________________<br>
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