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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Jennifer Hillman-Jackson
http://galaxyproject.org
___________________________________________________________
The Galaxy User list should be used for the discussion of
Galaxy analysis and other features on the public server
at usegalaxy.org. Please keep all replies on the list by
using "reply all" in your mail client. For discussion of
local Galaxy instances and the Galaxy source code, please
use the Galaxy Development list:
http://lists.bx.psu.edu/listinfo/galaxy-dev
To manage your subscriptions to this and other Galaxy lists,
please use the interface at:
http://lists.bx.psu.edu/
To search Galaxy mailing lists use the unified search at:
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