Non-commercial SNP calling soft

*#1* · 10-19-2010, 06:35 PM

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 · 10-19-2010, 09:01 PM

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 · 10-19-2010, 10:31 PM

See the Software Hub.

Boel · 10-20-2010, 02:27 PM

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!

rubence · 07-08-2012, 03:16 AM

Thanks great info , good dude !

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10-20-2010, 02:27 PM	#4
Boel Member Location: Stockholm, Sweden Join Date: Oct 2009 Posts: 62	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!

07-08-2012, 03:16 AM	#5
rubence Junior Member Location: Mumbai Join Date: Jul 2012 Posts: 1	Thanks great info , good dude ! __________________ Many jobs re available in plastics company,send resume here - jobs.plastemart.com , for top jobs with great salary .

10-19-2010, 06:35 PM	#1
#1 Junior Member Location: East coast Join Date: Jul 2010 Posts: 8	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

10-19-2010, 09:01 PM	#2
jgibbons1 Senior Member Location: Worcester, MA Join Date: Oct 2009 Posts: 133	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

10-19-2010, 10:31 PM	#3
nilshomer Nils Homer Location: Boston, MA, USA Join Date: Nov 2008 Posts: 1,285	See the Software Hub.