[ensembl-dev] variant effect predictor on bacteria genomes

[Will McLaren]

Hello,

Yes this is possible assuming you know the species name for the
bacteria you wish to use.

You can use the --genomes flag which is a shortcut that makes the
script connect to the Ensembl Genomes public server:

perl variant_effect_predictor.pl -i variants.vcf --genomes --species
[species_name]

Thanks

Will McLaren
Ensembl Variation

On 19 September 2012 10:55, Weihong Qi <Weihong.Qi at fgcz.ethz.ch> wrote:
> Dear Ensembl developers,
>
> Can the variant effect predictor (perl script) connect to Ensembl Bacteria
> genomes? If it does, what will the command line switches be?
>
> Thanks,
>
> Weihong
>
> --
> Weihong Qi, PhD
> Functional Genomics Center Zurich
> Uni/ETH Zurich
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>
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