I noticed that information on SNP calling and SNP discovery (especially!) software for NGS is quite scarce. Are there any good tools available from non-commercial sources? Could you suggest any titles (and corresponding URLs) one would want to look at? I am specifically looking for solutions for a robust secondary data analysis pipeline in a non-profit environment, for the data from virtually all platforms/read lengths, including 454, Illumina, SOLiD, and future platforms suich as PacBio, Ion Torrent, etc. Maybe we could start a list of such software here, with some details on which software is best for what kind of data. Thanks!
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I've found MAQ to be very good tool for SNP calling, but I'm not sure if it can handle larger reads. I use it with Illumina data.
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Gatk
Check out the genome analysis tool kit (GATK) developed at the Broad:
The UnifiedGenotyper is one of the task this toolkit has, but there are plenty of other great tools there. Good luck!
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