[ensembl-dev] output I get for my input file different when I use the web VEP and command line VEP

[Anja Thormann]

Hi Dayana,

thank you for the input file and web tool command line. I annotated your input file with both the web tool and command line VEP option and get for both output files 5519 SWISSPROT annotations if I grep for SWISSPROT. This is not the most in depth comparison. Could you please point me to some examples where you see a difference between the two annotation options?

The coordinates are always given for the Ensembl protein (ENSP...) which means you cannot use the protein position to look up the position in the SwissProt protein.

However, you shouldn’t see any differences between running with the VEP command line tool or the web online tool.

Thanks,
Anja

> On 28 Oct 2019, at 11:18, Dayana Yahalomi <dayana.yahalomi at weizmann.ac.il> wrote:
> 
> Hi Anja,
> This is the command from the web:
> ./vep --af --appris --biotype --buffer_size 500 --check_existing --distance 5000 --mane --polyphen b --pubmed --regulatory --sift b --species homo_sapiens --symbol --transcript_version --tsl --uniprot --cache --input_file [input_data] --output_file [output_file]
>  
> Attached is a vcf file.
>  
> Thanks,
> Dayana
>  
> From: Dev <dev-bounces at ensembl.org <mailto:dev-bounces at ensembl.org>> On Behalf Of Anja Thormann
> Sent: Monday, 28 October 2019 11:01
> To: Ensembl developers list <dev at ensembl.org <mailto:dev at ensembl.org>>
> Subject: Re: [ensembl-dev] output I get for my input file different when I use the web VEP and command line VEP
>  
> Dear Dayana,
>  
> could you please share which options you are using for the web tool? You can copy the command line equivalent from the job details section. Could you also please share an example for which you are seeing different annotations?
>  
> Thank you,
> Anja
> 
> 
> On 28 Oct 2019, at 07:06, Dayana Yahalomi <dayana.yahalomi at weizmann.ac.il <mailto:dayana.yahalomi at weizmann.ac.il>> wrote:
>  
> Dear Ensembl dev,
> I have installed the following vep program
> Versions:
>   ensembl              : 98.e98e194
>   ensembl-funcgen      : 98.36eef94
>   ensembl-io           : 98.052d23b
>   ensembl-variation    : 98.7b96c96
>   ensembl-vep          : 98.2
>  
> And When I run the following command (offline):
> ./vep --verbose --species homo_sapiens --assembly GRCh38 --offline --dir_cache=/bio/db/vep98 --input_file ex2.vcf --format vcf --output_file outputfile_uniprot.vep98.2_dayana2.vcf  --vcf --uniprot
>  
> I don’t get the same results as running the same file example in your web.
> I am interested in the protein changes and I look at the SwissProt flag. I used the protein name from SWISSPROT flag and go to the position indicated (Protein_position) and look if it is correct.
> In this case I get fewer protein changes and 30% are incorrect comparing to the web outfile where I get twice as much protein changes and only 10% are incorrect (this is probably due to different isoforms than the one in Swissprot).
> Do you know why I see these differences in the vcf outfile?
>  
> Thanks in advance,
> Dayana
>  
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