The publicly available IBS (Identity by State) macro in SAS is quite slow, and has a bug that IBS is not adjusted for call rate. I made an alternative implementation which is about 1/2 or 1/3 faster. However, SAS apparently handles the standard correlation calculations much much faster, and resulting Pearson correlation, Kendall correlation and Spearman correlation may give similar measurements to IBS (code is here, data include about 1000 markers clustered in candidate genes in 400 subjects, primary Caucasians). Therefor I guess in certain Kernel application, we can use usual correlation to replace IBS.
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