cnvkit_autobin - Quickly calculate reasonable bin sizes from BAM
read counts.
usage: cnvkit autobin [-h] [-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 ...]
- bams
- Sample BAM file(s) to test for target coverage
- -h, --help
- show this help message and exit
- -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.