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

[Dayana Yahalomi]

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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