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
___________________________________________________________ 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:
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-- Jennifer Hillman-Jackson http://galaxyproject.org