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.