I am interested in calculating LD and R^2 values for a region of interest using Haploview. I am interested in the data from phase 3 of the 1000 Genomes, so I have been loading the data in linkage format from .ped and .info files as downloaded from 1000 Genomes. My question is how the structure of the population (singletons versus family trios) influences LD analysis. When I load files with data from family trios, it treats them as singletons by default. Is it correct to conduct LD analysis with family trios, or should this be avoided?
The usual approach is to exclude all "nonfounders"--everyone who has a recorded ancestor also in the dataset, or who has e.g. a shared parent with another person in the dataset (even if said parent wasn't genotyped). (This is plink's default when calculating LD/r^2.)
The final Phase 3 release has had 31 known related individuals removed. Details of the removed individuals are provided in the release folder on the FTP site (/vol1/ftp/release/20130502/). The genotypes for these individuals can be found in the supporting subfolders.