[ensembl-dev] Fw: variant effect predictor script +Help

[Will McLaren]

Hi Neeba,

Currently the VEP only supports describing sequence variants (SNPs,
insertions, deletions, multi-bp substitutions) in HGVS format - to
enable this you just add the --hgvs flag when running the script.

If you wanted to retain the VCF format of your input, you can add the
flag --vcf. Furthermore, if, for example, you only want to add the
HGVS coding notation, and none of the consequence type fields, you
could add "--fields HGVSc", or "--fields HGVSp" for the protein
notation, or even "--fields HGVSc,HGVSp" to add both.

We do not yet support providing HGVS annotations for structural variants.

Hope this helps

Will McLaren
Ensembl Variation

On 11 July 2012 09:10, Neeba Sebastian <neeba.sebastian at calpinetech.com> wrote:
> Hi Team
>
> I am Using Variant Effect Predictor standalone script .
>
> I am trying to add HGVS notation to  the variants in vcf / or in default
> format.
>
> Is there any default argument or method to represents the structural
> variants in HGVS
>
> -- Thanks & Regards,
>
> Neeba Maria Sebastian
>
>
>
> ----- Forwarded Message -----
> From: Neeba Sebastian <neeba.sebastian at calpinetech.com>
> To: "dev at ensembl.org" <dev at ensembl.org>
> Sent: Wednesday, July 11, 2012 1:35 PM
> Subject: variant effect predictor script +Help
>
> Hi Team
>
> I am Using Variant Effect Predictor standalone script .
>
> I am trying to add HGVS notation to  the variants in vcf / or in default
> format.
>
> Is there any default argument or method to represents the structural
> variants in HGVS
>
> -- Thanks & Regards,
>
> Neeba Maria Sebastian
> Software Test Engineer
>
>
>
>
>
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