Here you can calculate linkage disequilibrium (LD) values between pairs of SNPs using data with known haplotypic phase.
You need to proceed as follows:
1. Enter a Description to identify the process in the top box.
2. Select the source of data to perform the LD calculation.
Phased data from PHASE* output files stored in the User Results
section. The haplotypes used will be those of the PHASE "report" file
and, when haploid samples were used, those of the "report.bis" file.
(See Run PHASE help for more info about "report.bis" files).
When the "report.bis" file assigns two possible haplotypes to haploid
samples, a unique haplotype will be generated containing blanks in
those SNPs differing between both haplotypes.
3. The resulting file (PhasedLDReport.txt) is sent to the User Results section.
It will contain:
- R squared
- Chi squared
Chi squared value from the 2x2 contingency table for each pair
P-value from the chi-square test applied to the 2x2 contingency
table for each pair of SNPs.
Not valid (N) when there is some expected value in the chi-
squared contingency table that is equal or below 1.
- Stephens, M., and Donnelly, P. (2003). A comparison of Bayesian methods for haplotype
reconstruction from population genotype data. American Journal of Human Genetics,