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Graham McVicker edited Basic Model.tex
over 9 years ago
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\subsection{Basic model}
The CHT is a likelihood ratio test
which models the data with two
components: components that model the read depth and
the allelic
imbalance. imbalance of the observed reads respectively. 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 respectively. alleles. Since variants are assumed to be additive and cis-acting, the expected allelic imbalance in heterozygotes, $p_h$,
can be calculated as is $p_h = \frac{\alpha_h}{\alpha_h + \beta_h}$ \cite{Sun_2011}.