Hello Debora,

There are no current plans to include additional genomes to the SnpEff tool on the public Main Galaxy instance at http://usegalaxy.org.


For the ANNOVAR tool, the supported genome at this time is "hg19". When a .vcf file is assigned to that reference genome (aka "database"), the tool form fills out to display the available annotation to select from. This tool is a brand-new implementation and still undergoing development, so I cannot comment yet about future plans.

The best solution is to either run a local Galaxy (with sufficient resources) or what is probably more practical for many scientific end users, a cloud Galaxy or possibly a Slipstream Appliance. The tool wrappers for both tools are in the Tool Shed, so it can be installed and used within your Galaxy, where you can add in any genome that you want that has the appropriate reference data available. The reference data formats can be found on the originating tool sites with supplemental help notes in the Tool Shed repositories.

Help to get started is in these links:
https://wiki.galaxyproject.org/BigPicture/Choices
https://wiki.galaxyproject.org/Tool%20Shed

Hopefully one of these solutions will work out you. If there is more to share, we will send a followup reply,

Jen
Galaxy team

On 2/24/14 3:39 AM, garzetti wrote:
Hallo Galaxy users,

I would like to annotate variants (in vcf file) found in my bacterial genomes and look which of them cause non-synonymous mutations. I have found two tools in the Main Galaxy that I can use for this purpose (snpEff and Annovar), but I have problems with them.

How can I change the input genome in snpEff? The only available choice in C. elegans. How can I choose my genome, already uploaded in my history?

Regarding Annovar, which file formats are required as Gene annotations/ Annotation Regions/ Annotation Databases? Reading the tool manual, it seems I can create my own txt/tabular files and use them for annotation, but the tool in Galaxy doesn't allow me to select any file, even if I have txt files in my history.

Any other suggested tool I can use?

Thanks!
Debora
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The Galaxy User list should be used for the discussion of
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