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

[Dan Sun]

Hi Will,

Thank you very much! That is super helpful.

Dan

On Mon, Jul 27, 2015 at 12:27 PM, Will McLaren <wm2 at ebi.ac.uk> wrote:

> 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:
>
> https://dl.dropboxusercontent.com/u/12936195/zonotrichia_albicollis.tar.gz
>
> And here's the long story, i.e. what I did to generate it if you want to
> do the same:
>
> wget
> ftp://ftp.ncbi.nlm.nih.gov/genomes/Zonotrichia_albicollis/GFF/ref_Zonotrichia_albicollis-1.0.1_scaffolds.gff3.gz
> wget
> ftp://ftp.ncbi.nlm.nih.gov/genomes/Zonotrichia_albicollis/CHR_Un/44394_ref_Zonotrichia_albicollis-1.0.1_chrUn.fa.gz
> 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
> zonotrichia_albicollis
>
> Then run the VEP as follows:
>
> perl variant_effect_predictor.pl -offline -species zonotrichia_albicollis
> -i variants.vcf
>
> Regards
>
> 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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>
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>


-- 
Dan Sun
Graduate student of Bioinformatics
School of Biology
Georgia Institute of Technology
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