Hello Maria, Good tool groups to start with are: "NGS: SAM Tools" and "NGS: Indel Analysis". Once you have SNP/Indel the coordinates in BED/Interval format, the tools in group "Operate on Genomic Intervals" can be used to compare the two datasets. Thanks for using Galaxy! Please let us know if you need more help, Jen Galaxy team On 10/11/11 10:34 AM, Gabriela Ronquillo-Lopez wrote:

Hello,

I am new using Galaxy, I would like ask if it is possible to perform a SNP and INDEL analysis between two SAM files (mutant and wt) with Galaxy. If so, could anyone give a hint in how to proceed?

Many thanks for your help in advance,

Kind regards,

Maria G.

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