<span id="mailbox-conversation"><div>Ahh, makes sense, thanks!</div></span><div class="mailbox_signature">
<br>-Konrad</div>
<br><br><div class="gmail_quote"><p>On Fri, Oct 31, 2014 at 5:19 AM, Will McLaren <span dir="ltr"><<a href="mailto:wm2@ebi.ac.uk" target="_blank">wm2@ebi.ac.uk</a>></span> wrote:<br></p><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;">
<div dir="ltr">Hi Konrad,<div><br></div>
<div>This is done so that particular HGVS notation doesn't break parsers working on the INFO field of VCF files (which have key1=value;key2=value2 etc).</div>
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<div>You can switch this off if you like with --no_escape</div>
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<div>Regards</div>
<div><br></div>
<div>Will McLaren</div>
<div>Ensembl Variation</div>
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<br><div class="gmail_quote">On 31 October 2014 05:12, Konrad Karczewski <span dir="ltr"><<a href="mailto:konradk@broadinstitute.org">konradk@broadinstitute.org</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div style="word-wrap:break-word">Hi dev team,<br><div><br></div>
<div>When outputting to VCF with --everything (implying --hgvs), the HGVS output for synonymous variants is p.%3D (i.e. the HTML code for equals is being printed out in the VCF) - is this supposed to be "p.="?</div>
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<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;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px"><br></div>
<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;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px">Thanks!<span class="HOEnZb"><font color="#888888"><br>-Konrad</font></span>
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