Bedtk: Finding Interval Overlap with Implicit Interval Tree

Abstract Summary We present bedtk, a new toolkit for manipulating genomic intervals in the BED format. It supports sorting, merging, intersection, subtraction and the calculation of the breadth of coverage. Bedtk employs implicit interval tree, a new data structure for fast interval overlap queries. It is several to tens of times faster than existing tools and tends to use less memory. Availability https://github.com/lh3/bedtk Contact hli@jimmy.harvard.edu , jiazhen_rong@hms.harvard.edu