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

Will McLaren wm2 at ebi.ac.uk
Tue Sep 27 13:30:13 BST 2016


In theory this should work, but the gtf2vep.pl script doesn't seem to work
too well with this particular GFF (it was designed really to work with
GFF/GTFs as produced by Ensembl or NCBI). Probably with some tweaks it
could be made to work - I believe the major issues are caused by features
being out of the order that the script expects.

The new code uses a much more robust system for constructing transcripts
and has been tested with GFFs from Ensembl, NCBI and GENCODE.

Will

On 27 September 2016 at 13:22, Konrad Karczewski <konradk at broadinstitute.org
> wrote:

> I just also realized - would creating a cache from this gff file (using
> gtf2vep.pl) not be recommended?
>
> -Konrad
>
> On September 27, 2016 at 5:16:42 AM, Will McLaren (wm2 at ebi.ac.uk) wrote:
>
> 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
>>
>> _______________________________________________
>> Dev mailing list    Dev at ensembl.org
>> Posting guidelines and subscribe/unsubscribe info:
>> http://lists.ensembl.org/mailman/listinfo/dev
>> Ensembl Blog: http://www.ensembl.info/
>>
>>
> _______________________________________________
> Dev mailing list Dev at ensembl.org
> Posting guidelines and subscribe/unsubscribe info:
> http://lists.ensembl.org/mailman/listinfo/dev
> Ensembl Blog: http://www.ensembl.info/
>
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mail.ensembl.org/pipermail/dev_ensembl.org/attachments/20160927/50fb4acf/attachment.html>


More information about the Dev mailing list