Bedtk: Finding Interval Overlap with Implicit Interval Tree

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/bedtkContact hli{at}jimmy.harvard.edu, jiazhen_rong{at}hms.harvard.eduCompeting Interest StatementThe authors have declared no competing interest.View Full Text