States and transition matrix of the HMM. A. This figure shows the definition of the states in the HMM. The genotype call for the germline DNA is given by the letter N = AB, AA or BB. For each state, the total DNA copy-number and the allelic copy-numbers are given. State 0 is the germline state also called the normal state; state 1 corresponds to a heterozygous deletion (loss of one allele); state 2 corresponds to a homozygous deletion (loss of two alleles); state 3 corresponds to uniparental di/polysomy (loss of one allele and duplication or multiplication of the other allele); state 4 corresponds to unbalanced amplification (duplication or multiplication of only one allele); state 5 corresponds to balanced amplification (duplication or multiplication of both alleles). Notice that when the SNP marker in the germline DNA is homozygous, states 3, 4 and 5 are very similar and states 0 and 3 cannot be differentiated in case of uniparental disomy. B. Visual interpretation of the states. C. Transition matrix. The transition probabilities are the probabilities to move from one state for a SNP to another state for the next SNP. The rest of the matrix is given by the detailed balance equation and symmetry. D. Visual interpretation of the transition parameters. The figure represents two consecutive SNPs in the sample.