[ensembl-dev] VEP ignoring --fasta option

[Ivan Adzhubey]

Hi,

I think there is an issue with the VEP script configuration processing: 
documentation states that you need both --hgvs and --fasta when --offline to 
trigger FASTA file reading from the local cache:

http://useast.ensembl.org/info/docs/tools/vep/script/vep_options.html#opt_hgvs

"To generate HGVS identifiers when using --cache or --offline you must use a 
FASTA file and --fasta."

However, when --everything option is specified, VEP would fetch alleles from 
the FASTA file available in the cache even in --offline mode and despite --fasta 
option *not* being used. Also, --fasta is not listed in the documentation as 
enabled by --everything implicitly either. However, it looks like it is 
enabled.

It would actually be nice to be able to have --fasta reading disabled (as per 
current documentation) even with --everything specified, especially considering 
dramatic performance degradation it causes and various stability problems with 
plugins. I am not sure if this is a bug report or a feature request but I 
really would love to see VEP script behave exactly like it is documented now: 
no --fasta option -- no FASTA cache reading. If that's not possible then the 
documentation should be corrected to describe the current behavior properly.

Thanks,
Ivan

-- 
Ivan Adzhubey, Ph.D.
Instructor
Division of Genetics, Dept of Medicine
Brigham & Women's Hospital
Harvard Medical School
New Research Building, Room 0464C
77 Avenue Louis Pasteur
Boston, MA 02115
tel.: (617) 525-4728
fax:  (617) 525-4705
web: http://genetics.bwh.harvard.edu/wiki/sunyaevlab/