Dprime, SNPGWA and Dandelion
Description
This group comprises three whole genome association tools from Wake Forest University:
- Dprime: This tool computes measures of linkage disequilibrium. It reads a data file of individual marker data and computes linkage disequilibrium statistics for all possible pairs of markers in the input file. Specific linkage dis-equilibrium statistics and format are determined by the input data and flags chosen.
- SNPGWA: This program reads diallelic marker data for case and control individuals from an input file and performs Hardy-Weinberg, genotypic association, linkage disequilibrium, allelic and two and three marker haplotype tests. Results of each test are written to an output file(s).
- Dandelion: This tool reads in a file of cases and controls, and uses the EM algorithm, assuming Hardy-Weinberg equilibrium, to estimate autosomal haplotype frequencies for both groups separately and jointly. Using these maximum likelihood haplotype frequency estimates, a likelihood ratio statistic is computed to determine whether there is heterogeneity in the observed haplotype frequencies between the cases and controls.
Availability
Installed on the cluster.
Please use `module load wfubmc` command to load the package binaries in your path in the BMI cluster.
Cost
Free
