Go Back   SEQanswers > Bioinformatics > Bioinformatics

Similar Threads
Thread Thread Starter Forum Replies Last Post
GATK snp calling wanguan2000 Bioinformatics 0 11-24-2011 09:23 PM
SNP calling pipeline golharam Bioinformatics 0 05-26-2011 09:20 AM
Samtools SNP calling vidhya Bioinformatics 3 04-07-2011 07:17 AM
SNP calling elondin Bioinformatics 3 01-24-2011 10:59 AM
SAMtools and SNP calling Jan Bioinformatics 2 09-16-2010 02:01 PM

Thread Tools
Old 10-19-2010, 06:35 PM   #1
Junior Member
Location: East coast

Join Date: Jul 2010
Posts: 8
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
*#1* is offline   Reply With Quote
Old 10-19-2010, 09:01 PM   #2
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.
jgibbons1 is offline   Reply With Quote
Old 10-19-2010, 10:31 PM   #3
Nils Homer
nilshomer's Avatar
Location: Boston, MA, USA

Join Date: Nov 2008
Posts: 1,285

See the Software Hub.
nilshomer is offline   Reply With Quote
Old 10-20-2010, 02:27 PM   #4
Location: Stockholm, Sweden

Join Date: Oct 2009
Posts: 62
Default 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!
Boel is offline   Reply With Quote
Old 07-08-2012, 03:16 AM   #5
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 - , for top jobs with great salary .
rubence is offline   Reply With Quote

polymorphisms, snp, snp calling, snp discovery

Thread Tools

Posting Rules
You may not post new threads
You may not post replies
You may not post attachments
You may not edit your posts

BB code is On
Smilies are On
[IMG] code is On
HTML code is Off

All times are GMT -8. The time now is 06:08 AM.

Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2021, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO