NoDear: No Disequilibrium Estimation of Accurate Recombination

Requirements

1. XGBoost
2. msprime

Please find the model and results in train-NoDear.ipynb.
Scripts to generate the simulated dataset are located in the ./simulation_scripts folder.
Scripts to run Pyrho are in the ./pyrho_scripts folder.
Scripts to obtain human genome data are in the ./human_genome_scripts folder.

Sequence of Actions

1. Simulate data (inside the ./simulation_scripts folder)
   (Please find the README file inside each subfolder.)

2. Get human genome data (inside the ./human_genome_scripts folder)
   (Please find the README file inside each subfolder.)

3. Run Pyrho (inside the ./pyrho_scripts folder)
   (Please find the README file inside each subfolder.)

4. Run train-NoDear.ipynb (runs XGBoost, produces results)

Citations:

Matthew W Hahn, Sarthak R Mishra, Estimating recombination using only the allele frequency spectrum, Genetics, 2025;, iyaf108, https://doi.org/10.1093/genetics/iyaf108