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\subsection{Basic model}  The CHT is a likelihood ratio test with two components: one to model the depth and the other to model the allelic imbalance of the mapped reads. Both components of the test are parameterized by $\alpha_h$ and $\beta_h$, which define the expected read depth from chromosomes with the reference and alternative alleles. Since variants are assumed to be additive and cis-acting, the expected allelic imbalance in heterozygotes, $p_h$, isdefined by  $p_h = \frac{\alpha_h}{\alpha_h + \beta_h}$ \cite{Sun_2011}.