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<div>Thanks a lot Will, this was very useful.</div>
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<div>Best wishes,</div>
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<div>Eva</div>
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<span style="font-weight:bold">From: </span>Will McLaren <<a href="mailto:wm2@ebi.ac.uk">wm2@ebi.ac.uk</a>><br>
<span style="font-weight:bold">Reply-To: </span>Ensembl developers list <<a href="mailto:dev@ensembl.org">dev@ensembl.org</a>><br>
<span style="font-weight:bold">Date: </span>Tuesday, 23 September 2014 09:21<br>
<span style="font-weight:bold">To: </span>Ensembl developers list <<a href="mailto:dev@ensembl.org">dev@ensembl.org</a>><br>
<span style="font-weight:bold">Subject: </span>Re: [ensembl-dev] VEP 76 build 37<br>
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<div dir="ltr">Hi Eva,
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<div>That should be enough to ensure the correct assembly. There is a --assembly flag that you can use to be sure.</div>
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<div>If you only have one cache installed for the software version (76) then it will be automatically used without the need for --assembly - check the headers in your output and you should see the cache directory. If you have two versions (i.e. both GRCh37
and GRCh38) then in --offline mode the VEP will prompt you to select one using --assembly.<br>
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<div>If you use --cache instead of --offline (which you might do in order to use rsIDs as input, for example), then you might also need to add "--port 3337" since on the default port VEP will use GRCh38. However, the VEP will warn you if the assembly version
of the database it connects to and the cache are different.</div>
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<div>See <a href="http://www.ensembl.org/info/docs/tools/vep/script/vep_other.html#assembly">http://www.ensembl.org/info/docs/tools/vep/script/vep_other.html#assembly</a> for more details of all of this.</div>
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<div>Regards</div>
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<div>Will McLaren</div>
<div>Ensembl Variation</div>
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<div class="gmail_quote">On 22 September 2014 17:19, Eva Goncalves Serra <span dir="ltr">
<<a href="mailto:egs@sanger.ac.uk" target="_blank">egs@sanger.ac.uk</a>></span> wrote:<br>
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<div>Hi, </div>
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<div>I have installed vEP 76 and downloaded the homo_<span style="font-style:italic">sapiens_</span>vep_<span style="font-style:italic">76</span>_37 cache files and the fasta Homo_sapiens.GRCh37.75.dna.primary_assembly.fa. </div>
<div>I want to make sure I am using the GRCh37 when using VEP. Do I need to specify anything in particular other than the cache dir? </div>
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<div>Thanks,</div>
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<div>Eva</div>
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