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

[Sarah Hunt]

Dear Paul,

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.

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.

Best wishes,

Sarah

On Wed, Jun 5, 2013 at 2:30 PM, Paul Denny <paul.denny3 at gmail.com> wrote:

> 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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