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<p class="MsoPlainText">Sorry - corrected the URL below.<o:p></o:p></p>
<p class="MsoPlainText"><o:p> </o:p></p>
<p class="MsoPlainText">The error now is:<o:p></o:p></p>
<p class="MsoPlainText"><o:p> </o:p></p>
<p class="MsoPlainText" style="margin-left:.5in">Unable to open/index remote VCF file: http://web.stanford.edu/group/dahlia_genetics/W23-1.unifiedSnpIndel.vcf.gz
<o:p></o:p></p>
<p class="MsoPlainText" style="margin-left:.5in">Ensembl can only display sorted, indexed VCF files
<o:p></o:p></p>
<p class="MsoPlainText" style="margin-left:.5in">Ensure you have sorted and indexed your file and that your web server is accessible to the Ensembl site
<o:p></o:p></p>
<p class="MsoPlainText" style="margin-left:.5in">For more information on the type of file expected please see the large file format documentation.<o:p></o:p></p>
<p class="MsoPlainText"><o:p> </o:p></p>
<p class="MsoPlainText"><o:p> </o:p></p>
<p class="MsoPlainText"><o:p> </o:p></p>
<p class="MsoPlainText"><o:p> </o:p></p>
<p class="MsoPlainText">-----Original Message-----<br>
From: feedback@gramene.org [mailto:feedback@gramene.org] <br>
Sent: Tuesday, March 7, 2017 2:48 PM<br>
To: feedback@gramene.org<br>
Cc: John Fernandes [Stanford University] <john.fernandes@stanford.edu><br>
Subject: Site Feedback: VCF custom track</p>
<p class="MsoPlainText"><o:p> </o:p></p>
<p class="MsoPlainText">URL : <a href="http://ensembl.gramene.org/Zea_mays/Info/Index">
<span style="color:windowtext;text-decoration:none">http://ensembl.gramene.org/Zea_mays/Info/Index</span></a><o:p></o:p></p>
<p class="MsoPlainText"><o:p> </o:p></p>
<p class="MsoPlainText">Subject : Site Feedback: VCF custom track<o:p></o:p></p>
<p class="MsoPlainText"><o:p> </o:p></p>
<p class="MsoPlainText">Name : John Fernandes<o:p></o:p></p>
<p class="MsoPlainText"><o:p> </o:p></p>
<p class="MsoPlainText">Email : <a href="mailto:john.fernandes@stanford.edu">
<span style="color:windowtext;text-decoration:none">john.fernandes@stanford.edu</span></a><o:p></o:p></p>
<p class="MsoPlainText"><o:p> </o:p></p>
<p class="MsoPlainText">Organization: Stanford University<o:p></o:p></p>
<p class="MsoPlainText"><o:p> </o:p></p>
<p class="MsoPlainText">Comments : <o:p></o:p></p>
<p class="MsoPlainText"><o:p> </o:p></p>
<p class="MsoPlainText">I am trying to upload a VCF customer track and getting an error that it cannot read it - file is not indexed. The VCF file was compressed with bgzip and indexed with tabit. Can you check why it is having trouble?<o:p></o:p></p>
<p class="MsoPlainText"><o:p> </o:p></p>
<p class="MsoPlainText">URL: <a href="http://web.stanford.edu/group/dahlia_genetics/W23-1.unifiedSnpIndel.vcf.gz">http://web.stanford.edu/group/dahlia_genetics/W23-1.unifiedSnpIndel.vcf.gz</a><o:p></o:p></p>
<p class="MsoPlainText"><o:p> </o:p></p>
<p class="MsoPlainText">An index file is present in same location.<o:p></o:p></p>
<p class="MsoPlainText"><o:p> </o:p></p>
<p class="MsoPlainText"><a href="http://www.warelab.org/bugs/view.php?id=5565"><span style="color:windowtext;text-decoration:none">http://www.warelab.org/bugs/view.php?id=5565</span></a><o:p></o:p></p>
<p class="MsoPlainText"><o:p> </o:p></p>
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