[ensembl-dev] discordant results between vep/cmd-line/conda and vep online.

[Diana Lemos]

Hi Pierre,

We strongly recommend that you use the VEP cache version which 
corresponds to your VEP installation, i.e. cache version 104. The 
version 91 is quite old.

You can download the cache from here: 
http://ftp.ensembl.org/pub/grch37/release-104/variation/indexed_vep_cache/


If that doesn't change the output consequence, you could also try to use 
the fasta file available here: 
http://ftp.ensembl.org/pub/grch37/release-104/fasta/homo_sapiens/dna/

Let me know if you have further questions.


Best wishes,

Diana



On 02/07/2022 13:08, Pierre LINDENBAUM wrote:
> Hi Ensembl,
>
> When I use our local vep installed via conda I got an intergenic 
> prediction for the following variant:
>
> ```
> module load ensembl-vep/104.3
>
> vep --cache --format vcf --force_overwrite --no_stats --offline 
> --dir_cache /LAB-DATA/BiRD/resources/apps/vep  --species homo_sapiens 
> --cache_version 91    --assembly GRCh37  --fasta 
> /LAB-DATA/BiRD/resources/species/human/cng.fr/hs37d5/hs37d5_all_chr.fasta 
> --use_given_ref --vcf  --output_file jeter2.vcf < jeter.vcf
>
>
> #CHROM    POS    ID    REF    ALT    QUAL    FILTER    INFO
> chr16    3016214    .    G    C    334.89    . 
> (...);CSQ=C|intergenic_variant|MODIFIER||||||||||||||||||||
> ```
>
> However, when using vep online, the variant is clearly a missense.
>
>
> ```
> | | 16:3016214-3016214 | C | missense_variant|
> ```
>
> what's wrong with my command-line ?
>
> thank you for your help !
>
>
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