deletions | additions       diff --git a/Modeling Allelic Imbalance.tex b/Modeling Allelic Imbalance.tex  index a91d919..49017bc 100644  --- a/Modeling Allelic Imbalance.tex  +++ b/Modeling Allelic Imbalance.tex 
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\subsection{Modeling the allelic imbalances}  Allele-specific read counts are sometimes modelled using the binomial distribution \cite{Reddy_2012}, 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 parameters, given the  datafor test $h$, $D_h$,  is then given by: then:  \[  \textrm{L}\left(\alpha_h, \beta_h \left| D \right. \right) = \prod_i \prod_k \Pr_{\mathrm{BB}} \left( Y = y_{ik} \left| n_{ik}, p_h, \Upsilon_i \right. \right) \\