CNVKIT-REFERENCE2TARGETS

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.

positional arguments:

reference

Reference file.

options:

-h, --help

show this help message and exit

-o OUTPUT, --output OUTPUT

Output base name (extensions added automatically).