Recombination

Recombination rates are specified per base, per generation. Can be specified for a slime.RecentHistory object via the recombination parameter.

Uniform recombination

Pass the rate to your slime.RecentHistory object via the recombination parameter.

For example, the following code indicates a recombination rate of 1e-8 per base per gen:

>>> script = slime.RecentHistory(final_gen=100, chrom_length=1e7,
...    recombination=1e-8, reference_configs=ref_pops, adm_configs=adm_pop,
...    prop=[0.3, 0.7])

Non-uniform recombination

A path to a space-delimited text file containing positions and rates can also be passed to the recombination parameter. The first column of the file should contain (ordered) integers representing base positions. The second column should contain recombination rates. The rate in the ‘n’th row is the per-base recombination rate for all bases between the base positions given in the `n`th (inclusive) and `n+1`th (not inclusive) row of the file.

Special rows: The position in the final row must be the length of the simulated sequence + n, but note that this row isn’t actually used (it’s a weird quirk of SLiM)… The first row is a header and will be ignored.

Here is an example of a valid recombination map for a sequence of length 10, with a recombination hotspot between bases 6 and 10:

position rate(cM/Mb)
1 0.1
6 0.5
11 0.1