Models
This model file format is based on admix simu’s.
Structure of a model.dat file
num_samples- Total number of samples to be output by the simulator (num_samples*2haplotypes)num_generations- Number of generations to simulate admixture, must be > 0*_freq- Frequency of populations to be present in the simulated samples
{num_samples} Admixed Pop_label1 Pop_label2 ... Pop_labeln
{num_generations} {admixed_freq} {pop_label1_freq} {pop_label2_freq} ... {pop_labeln_freq}
Example model.dat file
40 Admixed CEU YRI
6 0 0.2 0.8
Simulating 40 samples for 6 generations in this case implies the first generation has population freqs Admixed=0, CEU=0.2, YRI=0.8 and the remaining 2-6 generations have population frequency Admixed=1, CEU=0, YRI=0
Example pulse event model.dat file
40 Admixed CEU YRI
1 0 0.2 0.8
2 1 0 0
3 0.5 0.5 0
4 1 0 0
Simulating 40 samples for 4 generations in this case implies the first generation has population freqs Admixed=0, CEU=0.2, YRI=0.8 the second generation is purely admixed, the third has an event where a pure CEU population is introduced again at freqs Admixed=0.5, CEU=0.5, YRI=0 and finally we end with pure admixture.
More Example files
We have generated example model files that simulate current population structures within different populations in America as well as the Caribbean that can be found in the haptools repository here: haptools/example-files/models/ There are additional example model files that can be found in the haptools repository under haptools/tests/data/