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<p>Dear Michael,<br>
<br>
Which version of VEP 93 have you installed ?<br>
We put a fix about this NANS gene issue in the version 93.4
(<a class="moz-txt-link-freetext" href="https://github.com/Ensembl/ensembl-vep/releases/tag/release%2F93.4">https://github.com/Ensembl/ensembl-vep/releases/tag/release%2F93.4</a>).<br>
<br>
</p>
<p>For the transcript IDs which are an ID, we will have a look at
try to force it as a string.<br>
<br>
Best regards,<br>
</p>
<pre class="moz-signature" cols="72">Laurent</pre>
<div class="moz-cite-prefix">On 18/12/2018 23:46, Michael Yourshaw
wrote:<br>
</div>
<blockquote type="cite"
cite="mid:CANcs_J++-eOf=YZCw5=Hkqx8dEOh=f8-GLwjyDk1e10XdwPnXQ@mail.gmail.com">
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<div dir="ltr">I'm using VEP version 93, locally
installed with the cache.</div>
<div dir="ltr"><br>
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<div>This VCF input in the NANS gene:</div>
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<div> chr9 98056788 rs3199064 T G ...</div>
<div><br>
</div>
<div>yields the VEP json output:</div>
<div> ...,"gene_symbol":NaN,...</div>
<div><br>
</div>
<div>and fails a python script, which expects a
string, because an unquoted NaN is treated as
a float and casts to the string "nan".</div>
<div><br>
</div>
<div>A similar problem can happen when the
transcript_id looks like a number:</div>
<div> chr9 98056788 rs3199064 T G<br>
</div>
<div>yields</div>
<div> ...,"transcript_id":3494,...<br>
<div>In this latter case,
casting transcript_id as a string works, but
the need to cast is a trap for the unwary.</div>
<div><br>
</div>
<div>The json writer seems to be too clever
for its own good, as values that don't look
like numbers, such as "ENST00000495319" and
"IGHA2" have the expected double-quoting in
the json.</div>
<div><br>
</div>
<div>Indeed it seems odd that NANS becomes
float NaN, whereas NANP and other NAN* genes
remain proper json strings.</div>
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<div>ॐ<br>
Michael Yourshaw<br>
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