<html><head></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">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 variant_effect_predictor.pl -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 variant_effect_predictor.pl line 993.</div><div><div apple-content-edited="true"><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-variant: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-align: -webkit-auto; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; "><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><br></div><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">many thanks,</div><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><br></div><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">Paul</div></span></div></div></div></div></div><div apple-content-edited="true"><span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; 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