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Table 1 Run time of SeqSIMLA for generating family and case-control data

From: SeqSIMLA: a sequence and phenotype simulation tool for complex disease studies

 

1 Block

50 Blocks

(1,177 SNPs)

(55,681 SNPs)

Prevalence1

0.11

0.012

0.0014

0.11

0.012

0.0014

Family2

4.88 s

6.09 s

16.6 s

3.85 m

4.06 m

7.58 m

(94%)7

(76%)

(30%)

(82%)8

(76%)

(46%)

Family (T)3

4.58 s

5.33 s

7.52 s

3.35 m

3.45 m

4.51 m

(98%)

(91%)

(57%)

(87%)

(84%)

(67%)

Case-control4

3.17 s

4.86 s

26.35 s

3.10 m

3.75 m

11.01 m

(64%)

(33%)

(6%)

(34%)

(29%)

(11%)

Case-control (T)5

2.02 s

2.57 s

7.56 s

1.96 m

2.76 m

3.68 m

(88%)

(74%)

(20%)

(34%)

(37%)

(22%)

Case-control (F)6

2.42 s

2.44 s

2.27 s

1.95 m

1.87 m

1.87 m

(91%)

(91%)

(92%)

(58%)

(58%)

(58%)

  1. 1The estimated prevalence based on 10,000 prospective cohorts generated under Model 2.
  2. 2500 families generated with 1 thread.
  3. 3500 families generated with 12 threads.
  4. 41000 cases and 1000 controls generated with 1 thread.
  5. 51000 cases and 1000 controls generated with 12 threads.
  6. 61000 cases and 1000 controls generated with the conditional probability of multilocus genotypes given the disease status.
  7. 7Run time (seconds) and the percentage of run time spent on I/O.
  8. 8Run time (minutes) and the percentage of run time spent on I/O.