The Mapping Quality filter is activated by default. The filtering applies to the mapping quality of each SAM or BAM read. If the mapping quality of one of two reads in a pair is lower than the threshold, the entire pair is discarded. To allow an in-depth analysis of each filtering step, the product of the mapping quality filter, as well as the others, is stored in the Results path.

When a filter is turned off, the corresponding threshold input is grayed out and the Textbox inactivated to highlight the inactivation of the filter and avoid erroneous inputs.