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    <div class="moz-cite-prefix">Hello Konrad,<br>
      <br>
      Thanks, we're working on it now.<br>
      <br>
      Cheers,<br>
      <br>
      Daniel<br>
      <br>
      On 5/29/15 5:36 AM, Konrad Karczewski wrote:<br>
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      cite="mid:AFC25894-C88A-4909-9484-37877831CCAE@broadinstitute.org"
      type="cite">
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      <div class="">Hi Ensembl/VEP team,</div>
      <div class=""><br class="">
      </div>
      <div class="">Another corner case variant (yay!), though this one
        doesn't look as bad (or at least is obvious what's going on).
        Found the following variant (don't ask how):</div>
      <div class=""><br class="">
      </div>
      <div class="">2<span class="Apple-tab-span"
          style="white-space:pre"> </span>92326168<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>T</div>
      <div class=""><br class="">
      </div>
      <a moz-do-not-send="true"
href="http://genome.ucsc.edu/cgi-bin/hgTracks?db=hg19&highlight=hg19.chr2:92326168-92326168&position=chr2:92326123-92326212"
        class="">http://genome.ucsc.edu/cgi-bin/hgTracks?db=hg19&highlight=hg19.chr2%3A92326168-92326168&position=chr2%3A92326123-92326212</a>
      <div class=""><br class="">
      </div>
      <div class="">that happens to sit near a bunch of N's in the
        reference genome, which is throwing an error (I'm guessing in
        looking for motifs) as shown below.<br class="">
        <div class="">
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              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>
        </div>
        <br class="">
        <div class="">
          <div class="">-------------------- EXCEPTION
            --------------------</div>
          <div class="">MSG: Sequence GCTTNNNNNNNNNNNNN contains invalid
            characters: Only Aa Cc Gg Tt accepted</div>
          <div class="">STACK
            Bio::EnsEMBL::Funcgen::BindingMatrix::relative_affinity
/humgen/atgu1/fs03/konradk/vep/ensembl-tools-release-79/scripts/variant_effect_predictor/Bio/EnsEMBL/Funcgen/BindingMatrix.pm:301</div>
          <div class="">STACK
            Bio::EnsEMBL::Variation::MotifFeatureVariationAllele::motif_score_delta
/humgen/atgu1/fs03/konradk/vep/ensembl-tools-release-79/scripts/variant_effect_predictor/Bio/EnsEMBL/Variation/MotifFeatureVariationAllele.pm:226</div>
          <div class="">STACK
            Bio::EnsEMBL::Variation::Utils::VEP::mfva_to_line
/humgen/atgu1/fs03/konradk/vep/ensembl-tools-release-79/scripts/variant_effect_predictor/Bio/EnsEMBL/Variation/Utils/VEP.pm:2371</div>
          <div class="">STACK
            Bio::EnsEMBL::Variation::Utils::VEP::vfoa_to_line
/humgen/atgu1/fs03/konradk/vep/ensembl-tools-release-79/scripts/variant_effect_predictor/Bio/EnsEMBL/Variation/Utils/VEP.pm:2130</div>
          <div class="">STACK
            Bio::EnsEMBL::Variation::Utils::VEP::vf_to_consequences
/humgen/atgu1/fs03/konradk/vep/ensembl-tools-release-79/scripts/variant_effect_predictor/Bio/EnsEMBL/Variation/Utils/VEP.pm:1844</div>
          <div class="">STACK
            Bio::EnsEMBL::Variation::Utils::VEP::vf_list_to_cons
/humgen/atgu1/fs03/konradk/vep/ensembl-tools-release-79/scripts/variant_effect_predictor/Bio/EnsEMBL/Variation/Utils/VEP.pm:1373</div>
          <div class="">STACK
            Bio::EnsEMBL::Variation::Utils::VEP::get_all_consequences
/humgen/atgu1/fs03/konradk/vep/ensembl-tools-release-79/scripts/variant_effect_predictor/Bio/EnsEMBL/Variation/Utils/VEP.pm:1202</div>
          <div class="">STACK main::main
/humgen/atgu1/fs03/konradk/vep/ensembl-tools-release-79/scripts/variant_effect_predictor/variant_effect_predictor.pl:313</div>
          <div class="">STACK toplevel
/humgen/atgu1/fs03/konradk/vep/ensembl-tools-release-79/scripts/variant_effect_predictor/variant_effect_predictor.pl:144</div>
          <div class="">Date (localtime)    = Wed May 27 18:28:55 2015</div>
          <div class="">Ensembl API version = 79</div>
        </div>
      </div>
      <br>
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      <br>
      <pre wrap="">_______________________________________________
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</pre>
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