Hi-C Data Formats.

Processing, storing, and visualizing high-resolution Hi-C data required development of efficient data formats. A sparse matrix format saving only nonzero values has become the norm. A "zoomable" matrix style also became popular, storing multiple resolutions in a single file for interactive visualization. This chapter discusses the latest matrix file formats such as .hic and .mcool, and other intermediate formats including SAM/BAM and random-accessible contact lists.