Variant Detectors - filters

The variant detectors offer a number of filters. These relate both to which reads should be used, and how much evidence should be required for a variant to be called. The user is asked to set the values of these filters in two wizard steps: the 'General filters' step (figure 27.20) and the 'Noise filters' step (figure 27.21). Note that, for most of the filter, the values that they calculate and base their filtering on are also added as annotations to the variants (see Variant Detectors - the outputs). This means that they are available in the variant track and that the user can choose to perform the filtering in a post-processing step from the variant track table, rather than choosing to apply the filtering within the variant calling detection it self. The filters are described below.