Ensemble VEP difference web-version <=> command-line

Question

[ATpoint]

Did anybody ever encountered the situation that the VEP output differs when using the web version and the command line? In particular, the only thing that is different (but the most important info for me) is that I am missing the AF columns from the 1000Genomes project when using the command line version. The command line was exactly the same as in the web version, as copied from the "command line equivalent" field in the web output. Any suggestions?

==> UPDATE: After emailing the ensemble help desk, they said to have fixed the issue with the cache files which were apparently responsible for the problem. Replacing the old cache with the now updated one should solve the problem.

Answer 1

[Denise CS]

Have you used the --af flag for all populations from 1KG phase 3? Check the flags for the co-located variants that are not used by default.

[ATpoint]

That is the command:

./vep --af --af_1kg --af_esp --af_gnomad --appris --biotype --pubmed --regulatory --species homo_sapiens --symbol --tsl --cache

as copied from the output of the web version.