In Table 2, we compare PLINK 1.07 and PLINK 1.9 execution times under three scenarios: identity-by-state (IBS) matrix calculation only (–cluster –matrix –K [sample count - 1] in PLINK 1.07, –distance ibs square in PLINK 1.9), IBS matrix + standard clustering (–cluster –matrix for both versions), and identity-by-descent (IBD) report generation (–Z-genome.)Table 2 Identity-by-state (Hamming distance) and complete linkage clustering times (sec) CalculationDatasetMachinePLINK 1.07PLINK 1.90RatioIBS matrix onlysynth1pMac-22233.61.91.2 kMac-121320.41.21.1 kLinux32-81937.22.8690Linux64-51214923.7400Win32-23219.07.2450Win64-22674.41.51.8 ksynth2pMac-2∼190 k118.81.6 kMac-12∼99 k23.54.2 kLinux32-8152.5 k214.3710Linux64-512∼98 k25.33.9 kWin32-2∼270 k654.5410Win64-2∼200 k104.61.9 kchr1snpMac-2∼26 k17.51.5 kMac-1213.4 k12.61.06 kLinux32-818.4 k30.9600Linux64-512∼14 k43.1320Win32-232.7 k95.9341Win64-2∼26 k15.31.7 kBasic clusteringsynth1pMac-22315.72.7860Mac-121317.92.0660Linux32-81898.74.1460Linux64-51214964.5330Win32-23301.79.1360Win64-22724.51.91.4 ksynth2pMac-2∼230 k245.6940Mac-12∼140 k123.91.1 kLinux32-8197.1 k395.6498Linux64-512∼125 k143.3872Win32-2∼440 k976.7450Win64-2∼270 k127.92.1 kchr1snpMac-2∼26 k18.41.4 kMac-1213.6 k13.51.01 kLinux32-818.5 k33.4554Linux64-512∼14 k44.2320Win32-233.2 k95.0349Win64-2∼26 k15.81.6 kIBD reportsynth1pMac-22230.112.4180Mac-121346.22.4560Linux32-82019.912.4163Linux64-51214945.0300Win32-23446.342.281.7Win64-22669.815.1177synth2pMac-2∼190 k447.1420Mac-12∼99 k50.32.0 kLinux32-8161.4 k618.7261Linux64-512∼98 k57.41.7 kWin32-2∼270 k1801.1150Win64-2∼200 k541.0370IBD reportchr1snpMac-2∼26 k24.81.0 kMac-1213.4 k14.6918Linux32-818.5 k53.5346Linux64-512∼14 k46.5300Win32-233.1 k199.2166Win64-2∼26 k25.11.0 kComputation of the basic distance matrix is expensive, but has an “embarrassingly parallel” structure. Clustering requires an additional serial step, while the identity-by-descent report includes a pairwise population concordance test which does not benefit from bit-level parallelism, but speedups for both remain greater than 100x on 64-bit systems.
