What is the importance of r-squared for tagSNP selection?
The tagSNP selection is based on the extent of LD between the pairs of SNPs. This level of LD is measured in terms of an r-squared value and hence, varying values for r-squared will yield varying numbers of SNPs in the QuickSNP output. When r-squared=1 for two SNPs, they are said to be in perfect LD (and these two markers are redundant for genotyping), whereas an r-squared=0 indicates no LD. An r-squared of 0.8 is often used for tagSNP selection, as this value is felt to represent a compromise between completeness and efficiency of coverage of the common variation in the genome.
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