Linkage disequilibrium calculation, haplotype estimation and association Analysis
While there are now a lot of new programs for genomewide association analysis (GWAS) they form the basic elemements. These programs were in the Rockefeller list currently available from https://github.com/gaow/genetic-analysis-software
I have also converted some functionalities into R/gap available from CRAN (https://cran.r-project.org/).
2LD, EH+, FASTEH+, GENECOUNTING, HAP can be put in the same directory with call to the appropriate executables. EH+, FASTEH+ and GENECOUNTING can also share the same parameter and data file. I have tested them extensively under Windows, Sun, Dec Alpha and Linux systems. A brief comparison is shown in the following table. Program MCETDT (Monte Carlo module for the Extended Transmission Disequilibrium Test) is distributed with ETDT and unavailable from this site. Note to enter MS-DOS under the default setup for Windows Vista, you need to run c:\windows\system32\cmd.exe first.
| Package name | Executable names | Documentation | Features | Limitations |
|---|---|---|---|---|
| 2LD | 2ld |
2ld.doc, 2ld.htm |
D’, SE(D’), Cramer’s V for two multiallelic loci, r | Requires LDSHELL for many markers, does not show D’ in graphics |
| EH+ | eh, ehplus, fehp, pm, pmplus |
pm.doc, pm.stm |
Model-free and permutation tests of allelic association. EH compatible and very easy to use. (having been the top paper in Hum Hered in 2005/6/7). | Slower than FASTEH+ and GENECOUNTING but call FASTEH+ for permutation tests from version 1.2 |
| FASTEH+ | fpmp,fehp,pfehp |
fpmp.doc |
Faster algorithm and likelihood-based LD measures | Does not handle missing data, less statistics than EH+ |
| GENECOUNTING | gc,gcp,gcx,pgc |
gc.txt |
Haplotype frequency estimation and reconstruction, flexible in missing data patterns and X chromosome data, haplotype-specific tests | Limited to about 15 SNPs and slow with multiple multiallelic loci with missing data |
| HAP | hap,mia |
hap.txt |
Large number of SNPs and multiple imputations, missing data, multiallelic loci | Possibly sub-optimal solution |
2LD
Zhao, J. H. (2004). 2LD, GENECOUNTING and HAP: Computer programs for linkage disequilibrium analysis. Bioinformatics, 20, 1325-1326
Zapata C, Carollo C, Rodriguez S. (2001). Sampling variance and distribution of the D’ measure of overall gametic disequlibrium between multiallelic loci. Annals of Human Genetics, 65, 395-406
EH+
Zhao, J. H., Curtis, D., Sham, P. C. (2000). Model-free analysis and permutation tests for allelic associations. Human Heredity, 50(2), 133-139
FASTEH+
Zhao, J. H., Sham, P. C. (2002). Faster allelic association analysis using unrelated subjects. Human Heredity, 53(1), 36-41
GENECOUNTING
Zhao, J. H, .Lissarrague, S., Essioux, L., Sham, P. C. (2002). GENECOUNTING: haplotype analysis with missing genotypes. Bioinformatics, 18(12), 1694-1695.
Zhao, J. H. (2004). 2LD, GENECOUNTING and HAP: Computer programs for linkage disequilibrium analysis. Bioinformatics, 20, 1325-1326
HAP
Zhao, J. H. (2004). 2LD, GENECOUNTING and HAP: Computer programs for linkage disequilibrium analysis. Bioinformatics, 20, 1325-1326
The programs are available from https://github.com/jinghuazhao/Haplotype-Analysis.