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LD Pruning

7.13 LD Pruning

Overview

Some tests such as Identity by Descent and Inbreeding Coefficient Estimation will obtain better results if the markers used are not in linkage disequilibrium with each other.

Therefore, SVS provides this feature to deactivate (“prune”) markers that are in linkage disequilibrium with other markers that are left active, so that you may do your tests just with those active markers that are not as much in LD with each other.

Data Requirements

First, import your data into a SVS project (See Importing Your Data Into A Project) to create a genotypic spreadsheet. It is recommended that the spreadsheet be marker-mapped to insure that the markers are in the proper sequence. The samples in your spreadsheet are required to be rowwise. The LD Pruning dialog can be accessed by selecting Quality Assurance > Genotype > LD Pruning from the spreadsheet menu.

Method

All pairs of markers within a moving window, the size and increment of moving you may specify, are compared with each other to measure their pairwise LD. If any pair of markers which are both within the moving window are in LD greater than the specified threshold, the first marker of the pair will be deactivated (“pruned”).

Parameters

Window Size

Enter the window size in number of markers.

Window Increment

Enter the number of markers by which the beginning window position will be incremented.

LD r² threshold

For any pair of markers whose LD r² is larger than this, the first marker of the pair will be deactivated (“pruned”).

LD Computation Method

Check whether to use CHM or EM. CHM is computationally much faster, and gives almost the same results as the EM method.

End Result

The column deactivation will be on the spreadsheet you are working with, or on a new tab containing a copy of the spreadsheet you have been working with.