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

[Thomas Danhorn]

I suspect that the website uses assembly GRCh38 (at least by default), 
whereas you specified GRCh37 in your command line.  Since they are using 
different coordinate systems, you can't cut & paste coordinates from one 
to the other and doing so would result in the mismatch your see.

Best,

Thomas


On Sat, 2 Jul 2022, 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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