Applying peak shape filters to call peaks

The peak shape filter is then applied to the experimental data and a score is calculated at each genomic position. The score is obtained by extracting the genomic coverage profile of a window centered at the genomic position and then comparing this profile to the peak shape filter. The result of this comparison is defined as peak shape score. The peak shape score is standardized and follows a standard normal distribution, so a p-value for each genomic position can be calculated as $ {{\textrm{p-value} = \Phi(- \textrm{Peak shape score of the peak center})}}$, where $ \Phi$ is the standard normal cumulative distribution function.

Once the peak shape score for the complete genome is calculated, peaks are identified as genomic regions where the maximum peak shape score is greater than a given threshold. The center of the peak is then identified as the genomic region with the highest peak shape score and the boundaries are determined by the genomic positions where the peak shape score becomes negative.