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    <br>
    Hi Oliver,<br>
    <br>
    Thanks for the detailed report. This was a similar issue with a stop
    inserted before the stop not being handled well. It is fixed in
    branch78 so the consequence of the variant has changed from
    'stop_gained' to 'stop_retained'. The HGVS string reflects the
    synonymous status.<br>
    <br>
    Best wishes,<br>
    <br>
    Sarah<br>
    <br>
    <br>
    <div class="moz-cite-prefix">On 03/02/2015 16:52, Homann, Oliver
      wrote:<br>
    </div>
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cite="mid:D3A05613C476ED41995550C67C03CCAD2D022AAF@usso-pmsg-mbx04.am.corp.amgen.com"
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        <p class="MsoNormal"><span style="color:#1F497D">Apologies,
            forgot to clarify that the error occurs in line 1221 of the
            new version of TranscriptVariationAllele.pm:<o:p></o:p></span></p>
        <p class="MsoNormal"><span style="color:#1F497D"><o:p> </o:p></span></p>
        <p class="MsoNormal"><span style="color:#1F497D">   1221  
            unless( $hgvs_notation->{ref} eq "-"){<o:p></o:p></span></p>
        <p class="MsoNormal"><span style="color:#1F497D">   1222      
            $hgvs_notation->{ref}  =
            Bio::SeqUtils->seq3(Bio::PrimarySeq->new(-seq =>
            $hgvs_notation->{ref}, -id => 'ref',  -alphabet =>
            'protein')) || "";<o:p></o:p></span></p>
        <p class="MsoNormal"><span style="color:#1F497D">   1223   }<o:p></o:p></span></p>
        <p class="MsoNormal"><span style="color:#1F497D"><o:p> </o:p></span></p>
        <p class="MsoNormal"><span style="color:#1F497D">Regards,<o:p></o:p></span></p>
        <p class="MsoNormal"><span style="color:#1F497D">Oliver<o:p></o:p></span></p>
        <p class="MsoNormal"><span style="color:#1F497D"><o:p> </o:p></span></p>
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          <div style="border:none;border-top:solid #B5C4DF
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            <p class="MsoNormal"><b><span
style="font-size:10.0pt;font-family:"Tahoma","sans-serif";color:windowtext">From:</span></b><span
style="font-size:10.0pt;font-family:"Tahoma","sans-serif";color:windowtext">
                <a class="moz-txt-link-abbreviated" href="mailto:dev-bounces@ensembl.org">dev-bounces@ensembl.org</a> [<a class="moz-txt-link-freetext" href="mailto:dev-bounces@ensembl.org">mailto:dev-bounces@ensembl.org</a>]
                <b>On Behalf Of </b>Homann, Oliver<br>
                <b>Sent:</b> Tuesday, February 03, 2015 8:50 AM<br>
                <b>To:</b> Ensembl developers list<br>
                <b>Subject:</b> Re: [ensembl-dev] VEP (ver78)
                TranscriptVariationAllele.pm unitialized value error
                with --hgvs enabled<o:p></o:p></span></p>
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        <p class="MsoNormal"><o:p> </o:p></p>
        <p class="MsoNormal"><span style="color:#1F497D">Hello Sarah,<o:p></o:p></span></p>
        <p class="MsoNormal"><span style="color:#1F497D"><o:p> </o:p></span></p>
        <p class="MsoNormal"><span style="color:#1F497D">Your fix worked
            for all but one of my ‘uninitialized value’ errors.  Would
            you mind trying to track down the issue with this remaining
            problematic entry?<o:p></o:p></span></p>
        <p class="MsoNormal"><span style="color:#1F497D"><o:p> </o:p></span></p>
        <p class="MsoNormal"><span style="color:#1F497D">#CHROM            
            POS        ID            REF         ALT         QUAL   
            FILTER   INFO      FORMAT              SAMPLENAME<o:p></o:p></span></p>
        <p class="MsoNormal"><span style="color:#1F497D">19          
            42355761             rs374945441       C            
            CTAGAAA            885.10   .              
            AC=1;AF=5.556e-03;AN=180;BaseQRankSum=-1.922e+00;DB;DP=2670;FS=2.561;GQ_MEAN=75.28;GQ_STDDEV=91.16;InbreedingCoeff=-0.0056;MLEAC=1;MLEAF=5.556e-03;MQ=60.00;MQ0=0;MQRankSum=-2.160e-01;NCC=0;QD=9.83;ReadPosRankSum=0.353;SOR=0.669              

            GT:AD:DP:GQ:PL              0/0:17,0:17:34:0,34,505<o:p></o:p></span></p>
        <p class="MsoNormal"><span style="color:#1F497D"><o:p> </o:p></span></p>
        <p class="MsoNormal"><span style="color:#1F497D">Thanks,<o:p></o:p></span></p>
        <p class="MsoNormal"><span style="color:#1F497D">Oliver<o:p></o:p></span></p>
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