- Ignore broken pairs: When ticked, reads from broken pairs are ignored. Broken pairs may arise for a number of reasons, one being erroneous mapping of the reads. In general, variants based on broken pair reads are likely to be less reliable, so ignoring them may reduce the number of spurious variants called. However, broken pairs may also arise for biological reasons (e.g. due to structural variants) and if they are ignored some true variants may go undetected. Please note that ignored broken pair reads will not be considered for any non-specific match filters.
- Non-specific match filter: Non-specific matches are likely to come from repeat region whose exact mapping location is uncertain. In general, variants based on non-specific matches are likely to be less reliable. However, as there are regions in the genome that are entirely perfect repeats, ignoring non-specific matches may have the effect that true variants go undetected in these regions.
There are three options for specifying to which 'extent' the non-specific matches should be ignored:
- 'No': they are not ignored.
- 'Reads': they are ignored.
- 'Region': when this option is chosen no variants are called in regions covered by at least one non-specific match. In this case, the minimum length of reads that are allowed to trigger this effect has to be stated, as really short reads will usually be non-specific even if they do not stem from repeat regions.