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

[Pierre LINDENBAUM]

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 !