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.
- Minimum count (detection): Alleles observed in less than this number of reads will not be detected and can therefore not be reported.
- Minimum count (call): Alleles observed in less than this number of reads will not be called though will be reported as filtered if detected.
- Minimum allele fraction (detection): Alleles observed at less than this fraction will not be detected and can therefore not be reported.
- Minimum allele fraction (call): Alleles observed at less than this fraction will not be called though will be reported as filtered if detected.
- Minimum haplotype quality (detection): Haplotypes with lower quality will not be detected and can therefore not be reported.
- Minimum haplotype quality (call): Haplotypes with lower quality will not be called though will be reported as filtered if detected.
Figure 5.2: The Microhaplotype Caller general filters.