deletions | additions       diff --git a/QTL testing with WASP.tex b/QTL testing with WASP.tex  index e0f38b6..d047605 100644  --- a/QTL testing with WASP.tex  +++ b/QTL testing with WASP.tex 
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To discover molecular quantitative trait loci (QTLs) WASP uses a statistical test, which we call the Combined Haplotype Test (CHT). As input, CHT takes genotype probabilities at known SNPs as well as mapped reads from next-generation sequencing experiments such as ChIP-seq or RNA-seq. CHT combines two types of information from next generation sequencing data: the depth of mapped reads and the allelic imbalance of mapped reads that overlap heterozygous sites. CHT models the overdispersion of read counts (both across regions and across individuals) and accounts for variability introduced by GC content and the fraction of reads that fall within peaks.   We used an early version of CHT to discover histone mark QTLs \cite{McVicker_2013}. We have since  extended the statistical model, model  and made numerous improvements to the software implementation. These improvements include: \begin{itemize}  \item Automatic estimation of dispersion parameters from the data,  \item Adjustment for unknown covariates by allowing principal component loadings to be provided,