Coverage analysis

The coverage analysis tool is designed to identify regions in read mappings with unexpectedly low or high coverage. Such regions may e.g. be indicative of a deletion or an amplification in the sample relative to the reference. The algorithm fits a Poisson distribution to the observed coverages in the positions of the mapping. This distribution is used as the basis for identifying the regions of 'Low coverage' or 'High coverage'. The user chooses two parameter values in the wizard: (1) a 'Minimum length' and (2) a 'P-value threshold' value. The algorithm inspects the coverages in each of the positions in the read mapping and marks the ones with coverage in the lower or upper tails of the estimated Poisson distribution, using the provided p-value as cut-off. Regions with consecutive positions marked consistently as having low (respectively high) coverage, longer than the user specified 'Minimum length' value are called as 'Low coverage' (respectively 'High coverage') regions.

The coverage analysis tool may produce either an annotation track or a table, depending on the users choice, and, optionally, a report. The annotation track (or table) contains a row for each detected low or high coverage region, with information describing the location, the type and the p-value of the detected region. The p-value of a region is defined as the average of the p-values calculated for each of the positions in the region.