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 .