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Old 10-19-2010, 06:35 PM   #1
*#1*
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Exclamation Non-commercial SNP calling soft

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!

Last edited by *#1*; 10-19-2010 at 06:36 PM. Reason: typo
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Old 10-19-2010, 09:01 PM   #2
jgibbons1
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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.

http://maq.sourceforge.net/maq-man.shtml
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Old 10-19-2010, 10:31 PM   #3
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See the Software Hub.
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Old 10-20-2010, 02:27 PM   #4
Boel
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Default Gatk

Check out the genome analysis tool kit (GATK) developed at the Broad:
http://www.broadinstitute.org/gsa/wi...alysis_Toolkit

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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Old 07-08-2012, 03:16 AM   #5
rubence
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Thanks great info , good dude !
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polymorphisms, snp, snp calling, snp discovery

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