[ensembl-dev] Human Genome Build 36 VEP cache
Will McLaren
wm2 at ebi.ac.uk
Mon Aug 10 10:01:22 BST 2015
Hi Luke,
It just so happens I kept a copy of our last 36 build around for a request
like this :-)
You can download the cache file from here:
https://dl.dropboxusercontent.com/u/12936195/homo_sapiens_vep_54_NCBI36.tar.gz
After unpacking it in "$HOME/.vep", you will need to run VEP in offline
mode (--offline) and specify "--cache_version 54" to use it.
You will almost certainly find that a lot of options don't work or cause
VEP to crash, so use at your own risk, but it seems to work OK for basic
consequence types, which I assume is your use case.
$ echo "1 228912417 . A G" | perl variant_effect_predictor.pl
-cache_version 54 -offline -o stdout -no_stats | grep -v #
1_228912417_A/G 1:228912417 G ENSG00000135744 ENST00000366667
Transcript missense_variant 916 803 268 M/T
aTg/aCg - IMPACT=MODERATE;STRAND=-1
Regards
Will McLaren
Ensembl Variation
On 8 August 2015 at 13:59, <luke at well.ox.ac.uk> wrote:
> Dear Ensembl devs,
>
> I have a request about the VEP files available online.
>
> In attempting to analyse a large number of older .maf files with VEP, I
> couldn’t find a public cache for hg18 (build 36). Would it be at all
> possible to add this to the available genome caches? I would be incredibly
> grateful, as this would be a much neater fix than lifting over the
> coordinates (and losing information in the process).
>
> Many thanks,
> Yours faithfully,
>
> Luke Freeman-Mills
>
> PhD Student, MPG lab
> Oxford
>
>
>
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