deletions | additions       diff --git a/Modeling Allelic Imbalance.tex b/Modeling Allelic Imbalance.tex  index 2144d7a..3589375 100644  --- a/Modeling Allelic Imbalance.tex  +++ b/Modeling Allelic Imbalance.tex 
...
\subsection{Modeling the allelic imbalances}  Allele-specific read counts are sometimes modelled using the binomial distribution \cite{XXXX}, however, we have found that allele-specific read counts are overdispersed. We instead model allele-specific read counts with a beta-binomial (BB) distribution and estimate a parameter $\Upsilon_i$ that captures the overdispersion for each individual. The likelihood of the data for test $h$, $D_h$ $D_h$,  is then given by: \[  \textrm{L}\left( D_{h\bullet} \left| \alpha_h, \beta_h, \Upsilon_\bullet \right. \right) = \prod_i \prod_k \Pr_{\mathrm{BB}} \left( Y = y_{ik} \left| n_{ik}, p_h, \Upsilon_i \right. \right) \\