Read filters
The 'Read filters' determine which reads (or regions) should be considered when calling the variants.- 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.
- Non-specific match filter: Non-specific matches are likely to come from some type of repeat region, and the exact mapping location of them 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': when this option is chosen they are not ignored.
- 'Reads': when this option is chosen they are ignored.
- 'Region': when this option is chosen no variants are called in regions covered by at least one non-specific match.