More current research and software can be found at the eScience FaST-LMM site.

FaST-LMM (Factored Spectrally Transformed Linear Mixed Models) is a program for performing genome-wide association studies (GWAS) on large data sets. It runs on both Windows and Linux system, and has been tested on data sets with over 120,000 individuals [1,2].

  1. J. Listgarten*, C. Lippert*, C.M. Kadie, R.I. Davidson, E. Eskin, and D. Heckerman*. Improved linear mixed models for genome-wide association studies. Nature Methods, 9: 525-526, June 2012 (doi:10.1038/nmeth.2037). (*equal contributions)
  2. C. Lippert*, J. Listgarten*, Y. Liu, C.M. Kadie, R.I. Davidson, and D. Heckerman*. FaST linear mixed models for genome-wide association studies. Nature Methods, 8: 833-835, Oct 2011 (doi:10.1038/nmeth.1681). (*equal contributions)

Newer papers with improved algorithms can be found on the MSR eScience site for FaST-LMM.

Releases

Please go to the MSR eScience site for FaST-LMM for newer releases.

2012/05      - Future updates are now hosted on the MSR eScience site for FaST-LMM.

2012/04/06 - v1.09 - Several usability enahancements (MaxThreads), update to latest MKL libs (v10.3.7),
                                and misc fixes
2012/03/17 - v1.08 - Improve perf of SNC detection, add -extractSimTopK option, doc updates, 
                                -verboseOut fixes
2012/03/06 - v1.07 - Fix bug 17541 -sim option not processing the alternate phenotype file properly
2012/02/27 - v1.06 - Detection and filtering of constant genotypes in a SNP
                               + Bug fixes for binary and transposed files
2012/02/02 - v1.05 - Bug fixes
2012/01/05 - v1.04 - Add support for using dosage information + bug fixes
2011/11/21 - v1.03 - Add several perf enhancements relating -extract and -numjobs for improved
                                throughput and reduce memory usage
2011/09/27 - v1.02 - Add several perf enhancements relating to C++ for improved throughput and
                                reduce memory usage
2011/09/14 - v1.01 - Add -extract support to C# and small clean-up changes
2011/09/04 - v1.00 - Initial Release

 

Last edited Oct 4, 2013 at 9:07 PM by jennl, version 43