- Complex region
- A region with two or more overlapping loci.
- 'Countable' reads are sometimes also referred to as filtered reads. Which reads are 'countable' depends on the user settings when variant calling is performed - if e.g. the user has chosen 'Ignore broken pairs', reads belonging to broken pairs are not 'countable'.
- A DNA fragment that gives rise to a single read or read pair. Note that, although overlapping paired reads have two reads in their overlap region, they are only counted as one when counting fragments in that region.
- Variant Call Format. The file format specification can be found at GitHub https://samtools.github.io/hts-specs/ .