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cnvkit_autobin - Quickly calculate reasonable bin sizes from BAM read counts.


usage: cnvkit autobin [-h] [-f FILENAME] [-m {hybrid,amplicon,wgs}]

[--target-max-size BASES] [--target-min-size BASES] [--antitarget-max-size BASES] [--antitarget-min-size BASES] [--annotate FILENAME] [--short-names] [--target-output-bed FILENAME] [--antitarget-output-bed FILENAME] bams [bams ...]

positional arguments:

Sample BAM file(s) to test for target coverage


show this help message and exit
Reference genome, FASTA format (e.g. UCSC hg19.fa)
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.
Filename for target BED output. If not specified, constructed from the input file basename.
Filename for antitarget BED output. If not specified, constructed from the input file basename.
September 2022 cnvkit autobin 0.9.9