<div dir="ltr"><div class="gmail_extra"><div class="gmail_quote">On Wed, Dec 10, 2014 at 12:05 PM, Michael Heuer <span dir="ltr"><<a href="mailto:heuermh@gmail.com" target="_blank">heuermh@gmail.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"><div dir="ltr"><div><div><div><div><div><div><div><div>Hello,<br><br>I'm finally getting the chance to update some code that depends on the VEP REST endpoint from the beta version to the current production version and have a few questions. Looking specifically at this example<br><br><a href="http://rest.ensembl.org/vep/human/id/COSM476?content-type=application/json" target="_blank">http://rest.ensembl.org/vep/human/id/COSM476?content-type=application/json</a><br><br></div></div>Under transcript_consequences in this example somatic is "1,1,1". What is this supposed to represent? There are three colocated_variants, so I assume this is referring to that.<br></div><br></div>Under transcript_consequences allele_string="A/T" is now represented as variant_allele="T". It would be useful to have a similar reference_allele="A".<br></div></div></div></div></div></blockquote><div><br></div><div>I'm sorry, I might have this backward; COSMIC defines this variation as<br><div id="overview"><dt class=""><br></dt><dt class="">Mutation Id: COSM476
</dt><dt class="">AA Mutation: p.V600E ( Substitution - Missense )</dt>
<dt class="">CDS Mutation: c.1799T>A ( Substitution )</dt></div><a href="http://cancer.sanger.ac.uk/cosmic/mutation/overview?id=476">http://cancer.sanger.ac.uk/cosmic/mutation/overview?id=476</a><br><br></div><div>codons/amino_acids and HGVS appear correct but allele_string and variant_allele have it flipped, shouldn't allele_string be "T/A", variant_allele "A" and reference_allele "T"?<br></div><div dir="ltr"><br> "id": "COSM476",<br> "allele_string": "A/T",<br> <br> "transcript_consequences": [<br> {<br> "variant_allele": "T",<br><br> "codons": "gTg/gAg",<br> "hgvsc": "ENST00000479537.3:c.83T>A",<br><br> "amino_acids": "V/E",<br> "hgvsp": "ENSP00000418033.1:p.Val28Glu",<br> }<br><br> michael<br><div><div><div><div><div><div><div><div><div><br></div></div></div></div></div></div></div></div></div></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">
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