NAME

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

DESCRIPTION

       usage: cnvkit.py 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] [--target-output-bed FILENAME]
              [--antitarget-output-bed FILENAME] bams [bams ...]

   positional arguments:
       bams   Sample BAM file(s) to test for target coverage

   options:
       -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.

       --target-output-bed FILENAME
              Filename for target BED output. If not specified, constructed from the input file basename.

       --antitarget-output-bed FILENAME
              Filename for antitarget BED output. If not specified, constructed from the input file basename.

cnvkit.py autobin 0.9.10                            July 2023                                  CNVKIT_AUTOBIN(1)