table of contents
| CNVKIT_AUTOBIN(1) | User Commands | CNVKIT_AUTOBIN(1) |
NAME¶
cnvkit_autobin - Quickly calculate reasonable bin sizes from BAM read counts.
DESCRIPTION¶
usage: cnvkit autobin [-h] [-f FILENAME] [-m {hybrid,amplicon,wgs}]
- [-g FILENAME] [-t TARGETS] [-b BP_PER_BIN]
- [--target-max-size BASES] [--target-min-size BASES] [--antitarget-max-size BASES] [--antitarget-min-size BASES] [--annotate FILENAME] [--short-names] bams [bams ...]
positional arguments:¶
- bams
- Sample BAM file(s) to test for target coverage
optional arguments:¶
- -h, --help
- show this help message and exit
- -f FILENAME, --fasta FILENAME
- Reference genome, FASTA format (e.g. UCSC hg19.fa)
- -m {hybrid,amplicon,wgs}, --method {hybrid,amplicon,wgs}
- Sequencing protocol: hybridization capture ('hybrid'), targeted amplicon sequencing ('amplicon'), or whole genome sequencing ('wgs'). Determines whether and how to use antitarget bins. [Default: hybrid]
- -g FILENAME, --access FILENAME
- Sequencing-accessible genomic regions, or exons to use as possible targets (e.g. output of refFlat2bed.py)
- -t TARGETS, --targets TARGETS
- Potentially targeted genomic regions, e.g. all possible exons for the reference genome. Format: BED, interval list, etc.
- -b BP_PER_BIN, --bp-per-bin BP_PER_BIN
- Desired average number of sequencing read bases mapped to each bin. [Default: 100000.0]
- --target-max-size BASES
- Maximum size of target bins. [Default: 20000]
- --target-min-size BASES
- Minimum size of target bins. [Default: 20]
- --antitarget-max-size BASES
- Maximum size of antitarget bins. [Default: 500000]
- --antitarget-min-size BASES
- Minimum size of antitarget bins. [Default: 500]
- --annotate FILENAME
- 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.
| January 2021 | cnvkit autobin 0.9.8 |