Table 2.

Computation time of two software implementations to estimate kinship coefficients in three sets of GWAS SNP data

Summary of genome scan data				Computing time
Index	No. of SNPs	No. of samples	No. of pairs	KING	PLINK
1	3 079 857	269	36 046	2 min	2 h 9 min
2	324 748	602	180 901	1 min	1 h 13 min
3	549 338	2 454	3 009 832	25 min	28 h 30 min

The computation time refers to the time to estimate kinship coefficients for all pairs of individuals, excluding overhead costs such as the time to load data into the computer memory. The two KING implementations (the robust algorithm and the algorithm assuming homogeneous samples) took a similar amount of computational time. This computation time can be estimated reliably as the analysis time for the entire data minus the analysis time for only the within-family data. The unit of computation time is in minutes hours. All computation was performed on and Intel Xeon with 3.20 GHz processor.