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<p>Hi Margaret,</p>
<p>VEP focuses on variant annotation and doesn't perform lift overs.
We have an Assembly Converter web tool you may find useful:</p>
<p><a class="moz-txt-link-freetext" href="http://www.ensembl.org/Homo_sapiens/Tools/AssemblyConverter">http://www.ensembl.org/Homo_sapiens/Tools/AssemblyConverter</a></p>
<p>As you will see, this uses the Crossmap package, which you could
install locally if you are looking for a command line option.</p>
<p>Best wishes,</p>
<p>Sarah <br>
</p>
<div class="moz-cite-prefix">On 08/04/2020 17:59, Linan, Margaret
wrote:<br>
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<p class="MsoNormal">Hi, <o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">Can I get a example script for using
command line VEP to convert a hg19 VCF file to a VCF with
GRCh38 coordinates?<o:p></o:p></p>
<p class="MsoNormal">Also is it possible to include the
coordinates from hg19 in the GRCh38 lifted VCF file?<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">Best,<o:p></o:p></p>
<p class="MsoNormal">Margaret<o:p></o:p></p>
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