Demo: Running the Li & Stephens HMM on Simulated Data

Running mini_lshmm on simulated genomic data.

Li & Stephens HMM demo on msprime-simulated data. Panel A: Forward probability matrix showing the posterior over reference haplotypes at each site. Panel B: Viterbi path identifying the most likely copying template. Panel C: Posterior decoding probabilities along the genome. Panel D: True vs inferred copying source comparison.

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