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