Simulation Parameters
Controls switch probability between haplotypes (higher = more recombination)
Error Model
Probability of incorrect genotype call at each SNP
Actions
Phasing Accuracy
About HMM Phasing
Haplotype phasing determines which alleles are on the same chromosome.
Observed genotypes (e.g., 0/1) don't tell us the phase (0|1 vs 1|0).
Hidden Markov Model:
• Hidden states: Two phase configurations at each SNP
• Transition: Phase can flip with probability ~ recombination rate
• Emission: Observed genotype depends on current phase
• Viterbi algorithm: Finds most likely phase sequence
Switch errors: Positions where inferred phase flips incorrectly.
Phasing uses linkage disequilibrium patterns to statistically infer haplotypes.