[ensembl-dev] Ensembl release 82 is out!

[Will McLaren]

Hi Ivan,

You only need to use one of --database, --cache or --offline. Using
--offline implies using the cache.

If you use --offline, only the cache version matters. The data source and
algorithm versions listed in the header are consistent within a cache
version. The only other variable is the version of the VEP (and
corresponding API) that you are using, which is also listed in the header.

Regards

Will

On 6 October 2015 at 18:46, Ivan Adzhubey <iadzhubey at rics.bwh.harvard.edu>
wrote:

> 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/
>
>
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