Huge Variant and Reference Files Test

Input Files

gSearchANNOVARBEDTools
exact searchrange searchexact search range searchrange search
# of lines (data only)52,814,66552,557,64552,814,66552,557,64552,557,645
File size4.5GB4.5GB3.7GB3.7GB4.5GB

Reference Files

gSearchANNOVARBEDTools
exact searchrange searchexact search range searchrange search
# of lines (data only)39,706,715 3,807,839 39,706,715 3,807,839 3,807,839
File size6.6GB155MB1.2GB182MB184MB

Execution Time Summary

gSearchANNOVARBEDTools
exact searchrange searchexact search range searchrange search
Execution Time (sec)3471484,0011,27613,800

PC Specification

Product iMac MB953KH/A
CPU Intel Core i5 2.66GHz
# of cores
4
Memory 4GB (2GB * 2, 1067 MHz DDR3)

Typical Whole Genome Sequencing Variant File Test

Input Files

A dataset of 17 whole-genome sequences (CEPH/Utah Pedigree 1463 data). See Download page for more information.

Reference Files

gSearchANNOVAR
Exact match (1000g2010_CEU)Range search (sec) (tfbs)Exact match (1000g2010_CEU)Range search (sec) (tfbs)
# of lines (data only)7,725,663 3,807,839 7,725,663 3,807,839
File size265MB155MB160MB182MB

PC Specification

Product iMac MB953KH/A
CPU Intel Core i5 2.66GHz
# of core 4
Memory 4GB (2GB * 2, 1067 MHz DDR3)

Execution Time Summary

GenomeOperationgSearch (single-threaded)gSearch (multi-threaded)ANNOVAR
Exact search (sec)Range search (sec)Exact search (sec)Range search (sec)Exact search (sec)Range search (sec)
Average (3,845,133 lines, 381MB)Read data11.587.3711.597.3950.5751.17
Sort0.810.500.410.2681.4591.18
Search1.720.750.640.25
Write results5.024.164.853.97
Sum19.1412.7917.4911.87132.02142.35

Execution Time Details

GenomeOperationgSearch (single-threaded)gSearch (multi-threaded)ANNOVAR
Exact search (sec)Range search (sec)Exact search (sec)Range search (sec)Exact search (sec)Range search (sec)
GS12877 (3,830,403 lines, 380MB)Read data11.467.3011.437.2450.5551.10
Sort0.810.500.410.2781.1090.96
Search1.730.750.640.25
Write results5.024.064.723.77
Sum19.0212.6117.2011.53131.65142.06
GS12878 (3,904,269 lines, 387MB)Read data11.657.4811.647.4151.6051.00
Sort0.810.510.420.2781.7092.48
Search1.750.750.660.25
Write results5.074.144.883.91
Sum19.2812.8817.5911.84133.30143.48
GS12879 (3,909,320 lines, 388MB)Read data11.687.5011.737.5551.4251.00
Sort0.810.510.410.2781.9092.78
Search1.740.750.650.25
Write results5.104.154.783.90
Sum19.3312.9217.5711.97133.32143.78
GS12880 (3,901,545 lines, 387MB)Read data11.877.4111.737.3651.1651.10
Sort0.810.510.410.2782.1092.43
Search1.740.750.640.25
Write results5.064.154.864.20
Sum19.4812.8317.6512.07133.26143.53
GS12881 (3,888,670 linee, 386MB)Read data11.637.4111.617.4051.2451.00
Sort0.810.510.410.2781.8092.32
Search1.740.750.650.25
Write results5.114.235.053.87
Sum19.2812.9017.7211.78133.04143.32
GS12882 (3,898,677 lines, 387MB)Read data11.607.3811.607.5251.2451.10
Sort0.810.510.410.2782.0092.26
Search1.750.750.650.25
Write results5.124.224.804.00
Sum19.2812.8717.4712.04133.24143.36
GS12883 (3,883,072 lines, 385MB)Read data11.677.4811.607.3551.1351.40
Sort0.810.510.410.2781.3091.66
Search1.740.750.650.25
Write results5.044.104.873.93
Sum19.2612.8417.5311.79132.43143.06
GS12884 (3,822,445 lines, 379MB)Read data11.587.3511.527.2650.2351.00
Sort0.810.500.410.2681.3090.85
Search1.720.750.640.24
Write results4.984.174.743.83
Sum19.0912.7717.3111.59131.53141.85
GS12885 (3,801,784 lines, 377MB)Read data11.477.2811.527.4949.9751.20
Sort0.810.490.410.2580.9090.23
Search1.700.750.630.25
Write results4.994.294.733.85
Sum18.9712.8117.2911.84130.87141.43
GS12886 (3,747,040 lines, 371MB)Read data11.437.3411.497.2349.2051.10
Sort0.810.480.410.2580.6089.28
Search1.690.750.630.24
Write results4.874.014.793.94
Sum18.7912.5817.3211.67129.80140.38
GS12887 (3,762,638 lines, 373MB)Read data11.467.2511.497.3249.5951.30
Sort0.810.490.420.2680.6089.41
Search1.680.750.620.24
Write results4.924.104.853.96
Sum18.8812.5917.3811.78130.19140.71
GS12888 (3,866,738 lines, 384MB)Read data11.527.3411.547.4050.4351.10
Sort0.810.500.410.2782.0091.68
Search1.730.750.640.25
Write results5.144.195.124.10
Sum19.2012.7817.7212.01132.43142.78
GS12889 (3,643,266 lines, 361MB)Read data11.287.1311.367.1647.8851.10
Sort0.810.470.410.2480.0086.88
Search1.640.750.620.24
Write results4.613.984.613.86
Sum18.3412.3217.0011.51127.88137.98
GS12890 (3,906,044 lines, 388MB)Read data11.707.4211.587.5651.3551.20
Sort0.810.510.410.2781.8092.41
Search1.750.760.650.25
Write results5.194.274.954.04
Sum19.4412.9617.6012.11133.15143.61
GS12891 (3,879,467 lines, 385MB)Read data11.657.4211.677.6050.9151.30
Sort0.810.500.410.2681.6091.80
Search1.740.750.650.25
Write results5.074.204.914.00
Sum19.2712.8817.6412.10132.51143.10
GS12892 (3,827,308 lines, 380MB)Read data11.607.3711.677.4450.5451.60
Sort0.810.500.410.2681.7090.60
Search1.710.750.630.24
Write results4.974.204.804.06
Sum19.1012.8217.5112.01132.24142.20
GS12893 (3,894,582 lines, 386MB)Read data11.677.4511.747.3951.2651.30
Sort0.810.510.410.2782.2092.06
Search1.740.760.650.25
Write results5.144.334.954.28
Sum19.3713.0417.7512.19133.46143.36
Average (3,845,133 lines, 381MB)Read data11.587.3711.597.3950.5751.17
Sort0.810.500.410.2681.4591.18
Search1.720.750.640.25
Write results5.024.164.853.97
Sum19.1412.7917.4911.87132.02142.35