[ensembl-dev] VEP on 37, but Gencode 25?

[Will McLaren]

Hi Konrad,

The beta ensembl-vep code [1] supports annotation directly from a GFF file,
such as the one available from the GENCODE website [2].

$ curl
ftp://ftp.sanger.ac.uk/pub/gencode/Gencode_human/release_25/GRCh37_mapping/gencode.v25lift37.annotation.gff3.gz
| gzip -dc | grep -v "#" | sort -k1,1 -k4,4n -k5,5n | bgzip -c >
gencode.v25lift37.annotation.gff3.gz
$ tabix -p gff gencode.v25lift37.annotation.gff3.gz
$ perl vep.pl -i variants.vcf -gff gencode.v25lift37.annotation.gff3.gz
-fasta homo_sapiens.fa

This comes with limitations as the GFF file contains only the transcript
structure and not any of the additional annotations. However I do know of
someone successfully using LOFTEE with this exact setup.

Of course usual beta caveats apply, so if you do use it and find bugs
please report on the GitHub page.

Regards

Will McLaren
Ensembl Variation

[1] : https://github.com/willmclaren/ensembl-vep
[2] : http://www.gencodegenes.org/releases/25lift37.html

On 26 September 2016 at 20:40, Konrad Karczewski <konradk at broadinstitute.org
> wrote:

> Hi all,
>
> When running VEP 85 on GRCh37, I believe the process has been to annotate
> against Gencode 19 (the info.txt seems to confirm this). Realizing the
> ridiculousness of my request, is there any chance there is a cache floating
> around for Gencode 25lift37? Would go a long way for ExAC releases.
>
> Thanks!
> -Konrad
>
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