NAME¶

cnvkit-reference2targets - Extract target and antitarget BED files from a CNVkit reference file.

DESCRIPTION¶

usage: cnvkit-reference2targets [-h] [-o OUTPUT] reference

Extract target and antitarget BED files from a CNVkit reference file. Once you have a stable CNVkit reference for your platform, you can use this script to drop the "bad" bins from your target and antitarget BED files and avoid unnecessarily calculating coverage in those bins during future runs. This script is also useful to recover the target and antitarget BED files that match the reference if those BED files are missing or you're not sure which ones are correct.