What it does

This tool simulates an Illumina run and provides plots of false positives and false negatives. It allows for a range of simulation parameters to be set. Note that this simulation sets only one (randomly chosen) position in the genome as polymorphic, according to the value specified. Superimposed on this are "sequencing errors", which are uniformly (and randomly) distributed. Polymorphisms are assigned using the detection threshold, so if the detection threshold is set to the same as the minor allele frequency, the expected false negative rate is 50%.

Parameter list

These are the parameters that should be set for the simulation:

Read length (which is the same for all reads)
Average Coverage
Frequency for Minor Allele
Sequencing Error Rate
Detection Threshold
Number of Simulations

You also should choose to use either a built-in genome or supply your own FASTA file.

Output

There are one or two. The first is a png that contains two different plots and is always generated. The second is optional and is a text file with some summary information about the simulations that were run. Below are some example outputs for a 10-simulation run on phiX with the default settings:

Read length                    76
Average coverage               200
Error rate/quality score       0.001
Number of simulations          100
Frequencies for minor allele   0.002
                               0.004
Detection thresholds           0.003
                               0.005
                               0.007
Include summary file           Yes

Plot output (png):

Summary output (txt):

      FP              FN       GENOMESIZE.5386      fprate          hetcol          errcol
Min.   : 71.0   Min.   :0.0    Mode:logical     Min.   :0.01318         Min.   :0.004   Min.   :0.007
1st Qu.:86.0    1st Qu.:1.0    NA's:10          1st Qu.:0.01597         1st Qu.:0.004   1st Qu.:0.007
Median :92.5    Median :1.0    NA       Median :0.01717         Median :0.004   Median :0.007
Mean   :93.6    Mean   :0.9    NA       Mean   :0.01738         Mean   :0.004   Mean   :0.007
3rd Qu.:100.8   3rd Qu.:1.0    NA       3rd Qu.:0.01871         3rd Qu.:0.004   3rd Qu.:0.007
Max.   :123.0   Max.   :1.0    NA       Max.   :0.02284         Max.   :0.004   Max.   :0.007

False Positive Rate Summary
        0.003   0.005   0.007
0.001   0.17711 0.10854 0.01673
0.009   0.18049 0.10791 0.01738

False Negative Rate Summary
        0.003   0.005     0.007
0.001   1.0     0.8       1.0
0.009   0.4     0.7       0.9