Phased LD
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Here you can calculate linkage disequilibrium (LD) values between pairs of SNPs using data with known haplotypic phase.

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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.

3. The resulting file (PhasedLDReport.txt) is sent to the User Results section. It will contain:

- Pair
- D'
- R squared
- Chi squared
Chi squared value from the  2x2 contingency table for each pair of SNPs.
- P
P-value from the chi-square test applied to the 2x2 contingency table for each pair of SNPs.
- Validity
Not valid (N) when there is some expected value in the chi- squared contingency table that is equal or below 1.

References: