<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=""><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 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="">
<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="">-------------------- 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></body></html>