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, at least, this 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' are considered. The 'countable reads' are those that the user has not chosen to ignore. This means that, if the user, in the read filter, has specified that reads from broken pairs should be ignored, broken pair reads will not be countable. Similarly goes for the 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).
