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.
https://usegalaxy.org/u/galaxyproject/p/galaxy-101-ngs-variant

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:
https://vimeo.com/channels/galaxytoolshed

Hopefully this help you to get started.

Jen
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.

Thanks,
     Xiefan
University of Florida


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