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I forgot to mention that these are GRCh37 coordinates.
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<div class="">Bhavana<br class="">
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<div class="">Begin forwarded message:</div>
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<span style="font-family: -webkit-system-font, Helvetica Neue, Helvetica, sans-serif; color:rgba(0, 0, 0, 1.0);" class=""><b class="">From:
</b></span><span style="font-family: -webkit-system-font, Helvetica Neue, Helvetica, sans-serif;" class="">Bhavana Harsha <<a href="mailto:bh4@sanger.ac.uk" class="">bh4@sanger.ac.uk</a>><br class="">
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<span style="font-family: -webkit-system-font, Helvetica Neue, Helvetica, sans-serif; color:rgba(0, 0, 0, 1.0);" class=""><b class="">Subject:
</b></span><span style="font-family: -webkit-system-font, Helvetica Neue, Helvetica, sans-serif;" class=""><b class="">Possible bug in variation API - result different from VEP</b><br class="">
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<span style="font-family: -webkit-system-font, Helvetica Neue, Helvetica, sans-serif; color:rgba(0, 0, 0, 1.0);" class=""><b class="">Date:
</b></span><span style="font-family: -webkit-system-font, Helvetica Neue, Helvetica, sans-serif;" class="">11 July 2017 at 14:17:20 BST<br class="">
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</b></span><span style="font-family: -webkit-system-font, Helvetica Neue, Helvetica, sans-serif;" class=""><a href="mailto:dev@ensembl.org" class="">dev@ensembl.org</a><br class="">
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Hello,
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<div class="">For the following variant</div>
<div class="">17<span class="Apple-tab-span" style="white-space:pre"> </span>7576915<span class="Apple-tab-span" style="white-space:pre">
</span>7577019<span class="Apple-tab-span" style="white-space:pre"> </span>TGTTGGGCAGTGCTAGGAAAGAGGCAAGGAAAGGTGATAAAAGTGAATCTGAGGCATAACTGCACCCTTGGTCTCCTCCACCGCTTCTTGTCCTGCTTGCTTACC/-<span class="Apple-tab-span" style="white-space:pre">
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<div class="">the correct protein consequence for the transcript ENST00000269305 should be </div>
<div class="">ENSP00000269305.4:p.Ala307ThrfsTer34</div>
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<div class="">As is confirmed by the VEP web interface, REST API and the VEP perl script.</div>
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<div class="">However, when I try to get this using the Variation API, I get</div>
<div class="">ENSP00000269305.4:p.Ala307Thr</div>
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<div class="">This is how I’m using the API:</div>
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<div class=""><font face="Menlo" class="">$reg->load_registry_from_db(-host => '<a href="http://ensembldb.ensembl.org/" class="">ensembldb.ensembl.org</a>', -species => 'homo sapiens', -user => 'anonymous', -port => 3337);</font></div>
<div class=""><font face="Menlo" class="">my $sa = $reg->get_adaptor(‘human’, 'core', 'slice');</font></div>
<div class=""><font face="Menlo" class="">my $vfa = $reg->get_adaptor('human', 'variation', 'VariationFeature');</font></div>
<div class=""><font face="Menlo" class="">my $slice = $sa->fetch_by_region(‘chromosome', 17);</font></div>
<div class=""><font face="Menlo" class="">my $vf = Bio::EnsEMBL::Variation::VariationFeature->new(-start => 7576915, -end => 7577019, -slice => $slice, </font></div>
<div class=""><font face="Menlo" class=""><span class="Apple-tab-span" style="white-space:pre"></span>-allele_string => ‘TGTTGGGCAGTGCTAGGAAAGAGGCAAGGAAAGGTGATAAAAGTGAATCTGAGGCATAACTGCACCCTTGGTCTCCTCCACCGCTTCTTGTCCTGCTTGCTTACC/-‘, -strand => 1, -adaptor =>
$vfa);<span class="Apple-tab-span" style="white-space:pre"> </span></font></div>
<div class=""><font face="Menlo" class="">my $cons = $vf->get_all_TranscriptVariations;</font></div>
<div class=""><font face="Menlo" class="">my @hgvsp = grep { defined } map { $_->hgvs_protein } map { @{$_->get_all_alternate_TranscriptVariationAlleles} } @$cons;</font></div>
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<div class="">I’m using v89 for the API and the VEP script.</div>
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<div class="">Is there something I’m doing wrong in my script?</div>
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<div class="">Cheers,</div>
<div class="">Bhavana</div>
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Bhavana Harsha<br class="">
Bioinformatician<br class="">
COSMIC<br class="">
Wellcome Trust Sanger Institute<br class="">
Hinxton, UK<br class="">
CB10 1SA<br class="">
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