[ensembl-dev] using VEP71 with mus_musculus release 67?

[Paul Denny]

Dear VEP developers,

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? 

I've tried VEP 71, using this command:
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

but get error messages like this:

ERROR: Cache directory /Users/p.denny/.vep/mus_musculus/67/mus_musculus/71 not found at variant_effect_predictor.pl line 993.

many thanks,

Paul

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