General filters

There are three main properties by which the output can be filtered, and each of these have a detection and a call threshold (figure 5.2). The detection threshold specifies if elements are reported or not, whereas the call threshold specifies whether an element is marked with a filter to be disregarded as noise. Elements with applied filters are however still reported for inspection, which can be useful for evaluating borderline calls.

Image filters-general
Figure 5.2: The Microhaplotype Caller general filters.