Non-commercial SNP calling soft

[*#1*]

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!

[jgibbons1]

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.

http://maq.sourceforge.net/maq-man.shtml

[nilshomer]

See the Software Hub.

[Boel]

Gatk

Check out the genome analysis tool kit (GATK) developed at the Broad:

http://www.broadinstitute.org/gsa/wiki/index.php/The_Genome_Analysis_Toolkit

The UnifiedGenotyper is one of the task this toolkit has, but there are plenty of other great tools there. Good luck!

[rubence]

Thanks great info , good dude !