NAME

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

DESCRIPTION

       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 ...]

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

   optional arguments:
       -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.