[ensembl-dev] Ensembl release 82 is out!

[Ivan Adzhubey]

Hi Will,

On Tuesday, October 06, 2015 09:26:52 AM Will McLaren wrote:
> > One more question, here's the header excerpt from the example VCF
> > generated by
> > the test run:
> > 
> > $ head -7 example_annotated_GRCh37.vcf
> > ## ENSEMBL VARIANT EFFECT PREDICTOR v82
> > ## Output produced at 2015-10-05 20:54:32
> > ## Using cache in /net/data/vep/homo_sapiens/82_GRCh37
> > ## Using API version 82, DB version ?
> > ## polyphen version 2.2.2
> > ## sift version sift5.2.2
> > ## COSMIC version 71
> > 
> > Why the DB version is reported as missing (?) on line 4? Is this normal?
> > The cache path specified is correct.
> 
> If you are using --offline then the VEP script makes no DB connection, so
> the database version won't be checked. If you use --cache or --database
> then you will see the version populated. Perhaps it would be clearer to
> remove that statement from the header if no DB connection is made.

I did use the --cache option (together with --offline) to generate this 
particular VCF. Here is the complete command line used:

$ variant_effect_predictor.pl --offline --cache --dir /data/vep --assembly 
GRCh37 --format vcf -i /apps/vep/example_GRCh37.vcf --everything -o 
example_annotated_GRCh37.vcf

The reason I am asking is that we have found some discrepancies in the 
functional annotations for a number of variants/genes and would like to make 
sure correct version of the annotations database (i.e. the one installed in 
the local cache) is always used by the script.

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/