bgtools

bgtools is a set of utilities for performing commonly-needed operations on bedgraph files. It is not intended as a replacement for bedtools, and it does not re-implement functionality that bedtools already offers for bedgraph data.

Currently, bgtools offers the following sub-commands:

# For running a rolling mean or median
bgtools roll
# For getting genome-wide robust z-scores
bgtools robust_z
# For getting counts per million
bgtools cpm
# For writing contiguous regions of a bedgraph file to stdout in bed format
bgtools contiguous_regions
# For taking a bedgraph file with non-uniform bin widths and making them uniform
bgtools unify_widths

To get help documentation for bgtools, simply run bgtools --help. Likewise, to get help documentation for any subcommand, run bgtools <subcommand> --help, substituting the subcommand of interest for <subcommand>

Note that the above instructions assume the bgtools binary found in target/release is in your PATH environment variable.