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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="">
<div style="color: rgb(0, 0, 0); letter-spacing: normal;
orphans: auto; text-align: start; text-indent: 0px;
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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>
</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>
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</pre>
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