Supplemental Material for Tessele et al., 2025

Marker information of discovery and validation populations in HapMap format is included in files 'Discovery-Populations.hmp.txt' and 'Validation-Populations.hmp.txt'. The code to run the PCA analysis to eliminate outliers within families is found in 'PCA.R'. The code used to calculate linkage disequilibrium is found in 'C-Linkage_Disequilibrium_Loops.bach'. The code used to calculate the 2D-LD plots in discovery and validation families and the control plot is found in the `*_2D_LDplot.R' files. The 'Circleze.R' file has the code used to plot interchromosomal LD with chromosomes displayed circularly.