Simulate gene conversion on an arbitrary chromosome. Quiet for a while and not complete. Eventually I would like to gain some insight into chromosome-wide variation in GC content and other features as features affecting recombination vary.
The first target is simulating runs of homozygosity. Mutation creates heterozygosity, while gene conversion creates homozygous patches of varying size. What steady-state distributions of homozygosity runs can we expect?
- Sites are simulated as heterozygous (1) or homozygous (0).
- Mutational events occur at random.
- Double-stranded breaks (DSBs) also occur at random; direction and length of tract are draws as well.
TODO:
- 1000 and 10000bp chromosomes
- statistics at dynamic equilibrium
- statistics approaching equilibrium
- crossing over
- vary chromosome architecture
- Doxygen documentation on everything