NAME
cnvkit_target - Transform bait intervals into targets more suitable for CNVkit.
DESCRIPTION
usage: cnvkit.py target [-h] [--annotate ANNOTATE] [--short-names] [--split]
- [-a AVG_SIZE] [-o FILENAME]
-
interval
positional arguments:
- interval
-
BED or interval file listing the targeted regions.
options:
- -h, --help
-
show this help message and exit
- --annotate ANNOTATE
-
Use gene models from this file to assign names to the target regions. Format: UCSC refFlat.txt or ensFlat.txt file (preferred), or BED, interval list, GFF, or similar.
- --short-names
-
Reduce multi-accession bait labels to be short and consistent.
- --split
-
Split large tiled intervals into smaller, consecutive targets.
- -a AVG_SIZE, --avg-size AVG_SIZE
-
Average size of split target bins (results are approximate). [Default: 266.6666666666667]
- -o FILENAME, --output FILENAME
-
Output file name.