<div> </div>
<div>Dear Paul,</div>
<div> </div>
<div>We don't guarantee compatibility across different releases, so would generally recommend using the 67 version of VEP(2.5) with the 67 version cache files.</div>
<div> </div>
<div>If you wish to use the 67 cache files with code version 71, you could rename the directory from 67 to 71 and use  --dir /Users/p.denny/.vep to pick them up.</div>
<div> </div>
<div>Best wishes,</div>
<div> </div>
<div>Sarah<br><br></div>
<div class="gmail_quote">On Wed, Jun 5, 2013 at 2:30 PM, Paul Denny <span dir="ltr"><<a href="mailto:paul.denny3@gmail.com" target="_blank">paul.denny3@gmail.com</a>></span> wrote:<br>
<blockquote style="BORDER-LEFT:#ccc 1px solid;MARGIN:0px 0px 0px 0.8ex;PADDING-LEFT:1ex" class="gmail_quote">
<div style="WORD-WRAP:break-word">Dear VEP developers, 
<div><br>
<div>I have a pair of whole genome VCF format files in which variants were called against mus_musculus release 67 (assembly NCBI37 / mm9).  I have no opportunity to take the raw data and re-align to mouse 71.  I'd like to use VEP to look for the effects of the variants on genes and regulatory elements - can I use the latest version of VEP (71) or do I have to go back to versions 2.7 or 2.8? </div>

<div><br></div>
<div>I've tried VEP 71, using this command:</div>
<div>perl <a href="http://variant_effect_predictor.pl/" target="_blank">variant_effect_predictor.pl</a> -i /Volumes/MacExternal/P110202/WTCHG_26483.bam.vcf -o VEP_BALB.txt -fork 4 -offline --regulatory --species mus_musculus --cache --dir /Users/p.denny/.vep/mus_musculus/67 --chr 1</div>

<div><br></div>
<div>but get error messages like this:</div>
<div><br></div>
<div>ERROR: Cache directory /Users/p.denny/.vep/mus_musculus/67/mus_musculus/71 not found at <a href="http://variant_effect_predictor.pl/" target="_blank">variant_effect_predictor.pl</a> line 993.</div>
<div>
<div>
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<div style="WORD-WRAP:break-word"><br></div>
<div style="WORD-WRAP:break-word">many thanks,</div>
<div style="WORD-WRAP:break-word"><br></div>
<div style="WORD-WRAP:break-word">Paul</div></span></div></div></div></div></div>
<div><span style="TEXT-TRANSFORM:none;TEXT-INDENT:0px;BORDER-COLLAPSE:separate;FONT:medium Helvetica;WHITE-SPACE:normal;LETTER-SPACING:normal;WORD-SPACING:0px"><span style="TEXT-TRANSFORM:none;TEXT-INDENT:0px;BORDER-COLLAPSE:separate;FONT:medium Helvetica;WHITE-SPACE:normal;LETTER-SPACING:normal;WORD-SPACING:0px">
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<div style="WORD-WRAP:break-word"><span style="LINE-HEIGHT:normal;TEXT-TRANSFORM:none;FONT-VARIANT:normal;TEXT-INDENT:0px;BORDER-COLLAPSE:separate;WHITE-SPACE:normal;LETTER-SPACING:normal;WORD-SPACING:0px"><span style="TEXT-INDENT:0px"><span style="TEXT-INDENT:0px">
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<div style="FONT-STYLE:normal;FONT-FAMILY:Helvetica;FONT-SIZE:medium;FONT-WEIGHT:normal">Mobile:    <a href="tel:%2B44-07922078038" target="_blank" value="+447922078038">+44-07922078038</a></div>
<div>E-Mail:    <span> </span><a href="mailto:paul.denny3@gmail.com" target="_blank">paul.denny3@gmail.com</a></div>
<div style="FONT-STYLE:normal;FONT-FAMILY:Helvetica;FONT-SIZE:medium;FONT-WEIGHT:normal">Web:<span style="WHITE-SPACE:pre-wrap"> </span> <a href="http://www.gene-effects.co.uk/" target="_blank">http://www.gene-effects.co.uk</a></div>

<div style="FONT-STYLE:normal;FONT-FAMILY:Helvetica;FONT-SIZE:medium;FONT-WEIGHT:normal">Twitter:    <a href="http://twitter.com/pauldennyuk" target="_blank">http://twitter.com/pauldennyuk</a></div>
<div style="FONT-STYLE:normal;FONT-FAMILY:Helvetica;FONT-SIZE:medium;FONT-WEIGHT:normal">LinkedIn: <a href="http://uk.linkedin.com/in/pauldenny" target="_blank">http://uk.linkedin.com/in/pauldenny</a></div></div>
<div style="TEXT-TRANSFORM:none;BORDER-COLLAPSE:separate;FONT:medium Helvetica;WHITE-SPACE:normal;LETTER-SPACING:normal;WORD-SPACING:0px"><br></div></div></span><br></span><br></span></div></span></div></span></span></div>
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