[ensembl-dev] Human Genome Build 36 VEP cache

[luke at well.ox.ac.uk]

Dear Dr McLaren,

Apologies - seems to have been a temporary error. I have the file. Many
thanks again!

Luke


From: dev-bounces at ensembl.org [mailto:dev-bounces at ensembl.org] On Behalf
Of Will McLaren
Sent: 10 August 2015 10:01
To: Ensembl developers list
Subject: Re: [ensembl-dev] Human Genome Build 36 VEP cache

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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