Hello Oliver, You can compare SNP datasets using the tools under "RGENETICS" and "Human Genome Variation". dbSNP and 1000 Genomes data are locally cashed in our Libraries, making them easy to load into a history and use. Also, here is an example workflow that includes sample SNP analysis (dbSNP vs 1000 genomes): http://main.g2.bx.psu.edu/u/ericy/p/chry-1000-genomes Hopefully this helps, Best, Jen Galaxy team On 5/9/11 8:05 AM, Oliver, Gavin wrote:

Hi,

I am new to Galaxy and am wondering what tools are available for annotation of SNPs?

I know that snpEff is implemented in Galaxy and this enables annotation such as location and predicted effect, however I am wondering if there are any automated means of annotating a polymorphism as known/novel or determining its frequency in the population.

Does Galaxy offer anything like this or would it be necessary to create scripts that would for exampole compare to dbSNP for uniqueness and the 1000 genomes project for frequency.

Best,

Gavin

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