[ensembl-dev] Request to add one species to VEP pre-built cache

Will McLaren wm2 at ebi.ac.uk
Mon Jul 27 17:27:35 BST 2015

Hi Dan,

We have in fact just updated our GTF converter script to support GFF too
(get the new release, 81, for this capability).

However, giving it a go just now with that file I noticed the FASTA file
supplied doesn't play nicely with our indexer, so I tweaked the FASTA to
get it to run. Long story short, here's the cache:


And here's the long story, i.e. what I did to generate it if you want to do
the same:

gzip -dc 44394_ref_Zonotrichia_albicollis-1.0.1_chrUn.fa.gz | perl -e
'while(<>) { if(/^\>/) { $id = (split /\|/, $_)[3]; print "> $id\n";} else
{print}}' > 44394_ref_Zonotrichia_albicollis-1.0.1_chrUn.fa
perl gtf2vep.pl -i ref_Zonotrichia_albicollis-1.0.1_scaffolds.gff3.gz
-fasta 44394_ref_Zonotrichia_albicollis-1.0.1_chrUn.fa -species

Then run the VEP as follows:

perl variant_effect_predictor.pl -offline -species zonotrichia_albicollis
-i variants.vcf


Will McLaren
Ensembl Variation

On 27 July 2015 at 16:49, Dan Sun <meredithfy at gmail.com> wrote:

> Hi,
> I was trying to build a cache from GTF for white-throated sparrow by
> myself following the tutorial, but was not successful. If possible, could
> you please add this species to the download list? I would really appreciate
> that!
> You may download the GFF3 annotation for this species from NCBI ftp (
> ftp://ftp.ncbi.nlm.nih.gov/genomes/Zonotrichia_albicollis/GFF/ref_Zonotrichia_albicollis-1.0.1_scaffolds.gff3.gz)
> and convert it to GTF.
> Thank you very much!
> --
> Dan
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