Demo: Running Gamma-SMC on Simulated Data

Running mini_gamma_smc on simulated genomic data.

../../_images/fig_demo_gamma_smc.png — Gamma-SMC demo on msprime-simulated data. Panel A: True TMRCA vs Gamma-SMC posterior mean along the genome – the conjugate Bayesian filter tracks coalescence time changes. Panel B: Input heterozygosity track from a diploid genome simulated under a bottleneck. Panel C: Posterior precision (shape parameter) along the genome, with inset showing the relationship to coefficient of variation. Panel D: True vs inferred TMRCA scatter plot.

This figure was generated by running the mini_gamma_smc implementation on data simulated with msprime. The script is at figures/fig_demo_gamma_smc.py.