DOKK / manpages / debian 10 / cnvkit / cnvkit-autobin.1.en

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 ...]

Sample BAM file(s) to test for target coverage

show this help message and exit
Sequencing protocol: hybridization capture ('hybrid'), targeted amplicon sequencing ('amplicon'), or whole genome sequencing ('wgs'). Determines whether and how to use antitarget bins. [Default: hybrid]
Sequencing-accessible genomic regions, or exons to use as possible targets (e.g. output of
Potentially targeted genomic regions, e.g. all possible exons for the reference genome. Format: BED, interval list, etc.
Desired average number of sequencing read bases mapped to each bin. [Default: 100000.0]
Maximum size of target bins. [Default: 20000]
Minimum size of target bins. [Default: 20]
Maximum size of antitarget bins. [Default: 500000]
Minimum size of antitarget bins. [Default: 500]
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.
Reduce multi-accession bait labels to be short and consistent.
March 2019 cnvkit_autobin 0.9.5