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APPENDIX C: Running time details of BWA-GATK pipeline
Table 8: Detailed running time measure for BWA-GATK pipelines
Steps
Human 10x
Human 50x
Cow 12x
Rice - indica 30x
Rice - japonica
132x
Pig 8x
Pig 14x
Corn 11x
C6320
OPA
FC430
FDR
C6320
OPA
FC430
FDR
C6320
OPA
FC430
FDR
C6320
OPA
FC430
FDR
C6320
OPA
FC430
FDR
C6320
OPA
FC430
FDR
C6320
OPA
FC430
FDR
C6320
OPA
FC430
FDR
Aligning & Sorting
3.23
3.93
10.51
15.79
4.42
5.77
0.99
1.18
4.58
9.50
2.39
3.04
3.73
6.16
8.59
11.16
Mark/Remove
Duplicates
0.66
0.66
3.28
2.62
0.65
0.73
0.11
0.12
1.02
1.27
0.27
0.27
0.91
0.79
0.73
0.72
Generate
Realigning Targets
0.17
0.29
0.42
1.08
0.20
1.57
0.03
0.05
0.12
0.22
0.11
0.27
0.14
2.17
0.07
0.26
Realign around
InDel
2.25
2.50
7.65
8.90
2.46
3.15
1.07
1.25
5.62
7.37
1.67
1.83
2.51
5.02
2.76
3.18
Base Recalibration
0.99
1.82
4.12
6.80
1.19
1.96
0.30
0.36
1.46
3.16
0.70
1.01
1.08
3.74
0.79
1.91
HaplotypeCaller
3.74
4.52
8.75
10.28
8.10
9.33
1.55
1.77
5.70
8.95
8.01
14.65
9.11
16.02
8.87
16.72
GenotypeGVCFs
0.02
0.03
0.02
0.03
0.05
0.05
0.00
0.01
0.01
1.12
0.06
0.06
0.04
0.26
0.03
0.04
Variant
Recalibration
0.52
0.67
0.21
0.37
0.46
0.86
0.04
0.04
0.01
0.92
0.47
0.56
0.46
0.86
0.53
0.46
Apply Recalibration
0.02
0.04
0.01
0.04
0.03
0.06
0.00
0.01
0.00
0.03
0.05
0.08
0.03
0.06
0.02
0.05
Total Run Time
11.61
14.50
34.97
45.90
17.55
23.50
4.09
4.78
18.53
32.50
13.72
21.80
18.01
35.08
22.40
34.50
Number of
Genomes per Day
165
133
55
42
109
82
469
402
104
89
140
88
107
55
86
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