Hello Xiefan,

This page has a simple breakdown of how to call variants within Galaxy. This is brand new, so full annotation/video is pending, but it should still be straightforward to see how the data is prepped and which tools are used.

Another set of tutorial videos cover the tools, which you can use on the public site or on a scaled up cloud server as needed:

Hopefully this help you to get started.

Galaxy team

On 10/21/12 3:11 PM, Xiefan Fang wrote:
Dear galaxy users, 
    We have done deep sequencing on some known genomic loci using Hiseq2000. I have already mapped the reads to the reference sequences by using Galaxy. In the next step, I want to find SNPs and calculate the SNP percentage within the reads. There are 500,000 to 1,000,000 reads per biological sample. Can I do it with galaxy? If not, is there other programs available in windows? Considering that I am not very familiar with programming. 

University of Florida

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