Hi Sathya,

The SnpEff tool is set up at this time for annotation with the /C. elegans/ WS220 genome only. Including human in the future on the public Main server at http://usegalaxy.org is under current evaluation.


For now, use the tool in a local or cloud Galaxy instance, with the tool installed from the Tool Shed. Help to get started can be found here:
http://getgalaxy.org
http://usegalaxy.org/cloud
http://usegalaxy.org/toolshed

Take care,

Jen
Galaxy team

On 3/12/14 1:44 AM, Sathya wrote:
I am working on the project to predict SNP from NGS data. I have found SNP using SAM tools and GATK (used reference hg19). I would like to know effect of SNP using SNPeff in GALAXY. I have given SNP in vcf format. I could not change the genome option as human, it is set is C.elegans by default
Please help me to solve this



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With regards,
Sathya.B



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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

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To search Galaxy mailing lists use the unified search at:

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