These filters specify absolute requirements for the variants to be called. Note that suitable values for these filters are highly dependent on the coverage in the sample being analyzed:
- Minimum coverage: Only variants in regions covered by at least this many reads are called.
- Minimum count: Only variants that are present in at least this many reads are called.
- Minimum frequency: Only variants that are present at least at the specified frequency (calculated as 'count'/'coverage') are called.
These values are calculated for each of the detected candidate variants. If the candidate variant meets the specified requirements, it is called. Note that when the values are calculated, only the 'countable reads' - the reads chosen by the user to NOT be ignored - are considered. For example, if the user had specified to ignore reads from broken pairs, they will not be countable. This is also the case for non-specific reads, and for reads with bases at the variant position that does not fulfill the base quality requirements specified by the 'Base Quality Filter' (see the section on 'Noise filters' below).
Also note that overlapping paired reads only count as one read since they only represent one fragment.