[ensembl-dev] Help with VEP options

[Will McLaren]

Hello,

On Macs sometimes zcat or gzip behave differently to other UNIX
systems - can you try adding the flag:

--compress "gunzip -c"

when you run the script?

Regarding SIFT and PolyPhen in VCF format, there is an issue with the
VCF format that I have yet to solve. VCF specifies one line per
variant; however, the VEP produces predictions not only per variant
but for each transcript that the variant overlaps. Thus a single
variant will frequently have multiple SIFT and PolyPhen predictions,
each one specific to a transcript - basically I haven't come up with a
sensible way of writing this data in the VCF INFO field without it
getting really messy!

If you have a suggestion for how to do this then I'd certainly take it on board.

In the meantime you can use the default output format of the VEP to
retrieve SIFT and PolyPhen predictions.

Thanks

Will McLaren
Ensembl Variation

On 1 February 2012 17:44, Paila, Uma Devi (udp3f)
<udp3f at eservices.virginia.edu> wrote:
> Hi developers of VEP,
>
> It was great using the latest version of your tool  (v2.3) 'Variant effect
> Predictor'  which looks promising. We were actually interested in the
> standalone version of your software but encountered some issues when trying
> to use the script with the —cache option on mac. There was some issue with
> the reading of the transcript data  in the cache, though gzip and zcat
> utilities were installed on the local machine (basically a mac environment
> and not linux). The errors that I get are:
>
> ~/.vep/homo_sapiens/65/1/1-1000000.gz.Z: No such file or directory
>
> Magic number checking on storable file failed
>
> We were wondering if that could be fixed by some means. It would be a great
> help!
>
> Secondly, if we understand correctly, the –sift and –polyphen options were
> lately introduced and are not in terms with the –vcf option. It would have
> been great if we could see the polyphen and sift predictions under 'CSQ' of
> an output vcf file, when we choose the three output options as;
> --sift —polyphen —vcf
> We understand it has been clearly documented that the –vcf option only
> displays consequence type, but it would be of great use if the —vcf option
> was available in conjugation with the —sift and —polyphen options. Please
> let us know if you could make that option available to us.
>
> Regards,
>
> Uma D.Paila (Ph.D),
> Research Associate with Dr. Aaron Quinlan,
> Center for Public Health Genomics,
> University of Virginia, VA
>
> _______________________________________________
> Dev mailing list    Dev at ensembl.org
> List admin (including subscribe/unsubscribe):
> http://lists.ensembl.org/mailman/listinfo/dev
> Ensembl Blog: http://www.ensembl.info/
>