GCTA

a tool for Genome-wide Complex Trait Analysis

Executable Files

gcta_1.0.zip

Linux 32-bit: gcta

Linux 64-bit: gcta64

MS-DOS 32-bit: gcta.exe

Mac OS: gcta_mac

Source code

gcta_0.93.9.src.zip

Documentation

 GCTA_UserManual_v1.0.pdf

Update log

1. 30 Aug, 2010: first release.
2. 17 Sep, 2010: fixed a bug in the estimation of LD and compiled the program statically (more compatible) 
3. 11 Oct, 2010: fixed a bug in transforming the estimate of variance explained by the SNPs on the observed scale to that on the underlying scale for a case-control study.
4. 13 Oct, 2010: MacOS version released.
5. 14 Oct, 2010: fixed a bug in reading the PLINK FAM file.
6. 23 Nov, 2010: source codes released.
7. 24 Dec, 2010: added a few new functions, e.g. convert the raw genotype data into PLINK binary format.
8. 10 Feb, 2011: fixed a few bugs.
9. 24 Mar, 2011: modified the output of LD estimation and the input format of GWAS simulation
10. 2 Apr, 2011: fixed a bug in a REML analysis, i.e. the estimate may be stuck at zero if the true parameter is very small.
11. 8 Apr, 2011: fixed a bug in GWAS simulation.
12. Version 0.93.0 (8 Jul 2011): added a subroutine to deal with the issue when the variance-covariance matrix V is negative-definite; changed the default number of maximum REML iterations from 30 to 100; changed the method of calculating the diagonal elements of GRM to be the same as that for the off-diagonal elements; modified REML procedure to allow some elements of the GRM to be missing (printing a warning on the screen in stead of an error message).   
13. Version 0.93.1 (12 Jul 2011): improved the efficiency of reading PLINK binary data. 
14. Version 0.93.2 (18 Jul 2011): fixed a bug in the matrix bending subroutine.
15. Version 0.93.4 (15 Aug 2011): added a function to calculate the LRT for the REML analysis.
16. Version 0.93.5 (26 Aug 2011): added an option to turn off the LRT and fixed a bug in the case that the IDs of multiple GRM files are not in the same order.
17. Version 0.93.6 (28 Aug 2011): fixed a bug in the new option --reml-lrt which caused memory leak.
18. Version 0.93.7 (10 Sep 2011): fixed a bug when the option --ibc is used in combined with the option --keep or --remove, which causes wrong IDs in the *.ibc fie; fixed a bug in --gxe option when there are missing values for the environmental factor; and modified the function for converting Illumina raw genotype data to that in PLINK format.
19. Version 0.93.8 (30 Sep 2011): fixed a bug for the option --grm-adj when the genotype data of some individuals are completely missing.
20. Version 0.93.9 (18 Nov 2011): modified the --dosage-mach option to be compatiable with the latest MACH version; fixed a bug with the option --ld.
21. 30 Nov 2011: latest version (version 0.93.9) of source codes released.
22. 14 May 2012: version 1.0 released!