[ensembl-dev] command line VEP with old Ensembl database

[Will McLaren]

Hi Shawn,

The v65 cache included SIFT and PolyPhen scores (
ftp://ftp.ensembl.org/pub/release-65/variation/VEP/homo_sapiens/) but I've
just given it a quick test with v80 code and it fails if you try to use
SIFT or PolyPhen.

You might have some luck hacking the info.txt file in that cache file once
you've unpacked it to ~/.vep/, something like:

echo "source_polyphen 2.2.2|source_sift sift5.2.2" | tr "|" "\n" | tr " "
"\t" >> ~/.vep/homo_sapiens/65/info.txt

and then running VEP as e.g.:

perl variant_effect_predictor.pl -i example_GRCh37.vcf -offline
-cache_version 65 [etc]

If you are able, it is always safer to match software to data version, so
if you can use v65 of VEP (and the API that goes with it), then that's
safest. You can either download the relevant version from GitHub, or use
git itself to checkout release/65 branches of ensembl-tools, ensembl,
ensembl-variation and ensembl-funcgen

Regards

Will McLaren
Ensembl Variation



On 13 June 2015 at 08:57, Shawn Yost <Shawn.Yost at icr.ac.uk> wrote:

> Hi,
>   Is there a way to run the current version of VEP (with SIFT and PolyPhen
> scores) on an older version of Ensembl (specifically Ensembl v65)?
>
> Thank you,
>   Shawn Yost
>
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