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| CNVKIT_TARGET(1) |
User Commands |
CNVKIT_TARGET(1) |
NAME¶
cnvkit_target - Transform bait intervals into targets more suitable for CNVkit.
DESCRIPTION¶
usage: cnvkit target [-h] [--annotate ANNOTATE] [--short-names] [--split]
- [-a AVG_SIZE] [-o FILENAME]
- interval
positional arguments:¶
- interval
- BED or interval file listing the targeted regions.
optional arguments:¶
- -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.
