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.
optional arguments:¶
- -h, --help
- show this help message and exit
- -o OUTPUT, --output OUTPUT
- Output base name (extensions added automatically).