[ensembl-dev] VEP ignoring --fasta option

[Will McLaren]

Hi Ivan,

The VEP will auto-detect a FASTA file in your cache directory, which is
presumably what is being used when you specify --everything without --fasta.

There's currently no way to disable this auto-detection; the easiest thing
to do would be to remove or move the file (typically
$HOME/.vep/homo_sapiens/84_GRCh38/*.fa)

You could alternately manually list the options set by --everything,
excluding --hgvs as this is what uses the sequence lookups.

Hope that helps,

Will McLaren
Ensembl Variation

On 8 April 2016 at 18:47, Ivan Adzhubey <iadzhubey at rics.bwh.harvard.edu>
wrote:

> 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/
>
>
> _______________________________________________
> Dev mailing list    Dev at ensembl.org
> Posting guidelines and subscribe/unsubscribe info:
> http://lists.ensembl.org/mailman/listinfo/dev
> Ensembl Blog: http://www.ensembl.info/
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mail.ensembl.org/pipermail/dev_ensembl.org/attachments/20160411/752c8e1b/attachment.html>