NAME

       cnvkit - a command-line toolkit for copy number analysis.

DESCRIPTION

       usage: cnvkit [-h]

              {batch,target,access,antitarget,autobin,coverage,reference,fix,segment,call,diagram,scatter,heatmap,breaks,genemetrics,gainloss,sex,gender,metrics,segmetrics,bintest,import-picard,import-seg,import-theta,import-rna,export,version}
              ...

       CNVkit, a command-line toolkit for copy number analysis.

   positional arguments:
       {batch,target,access,antitarget,autobin,coverage,reference,fix,segment,call,diagram,scatter,heatmap,breaks,genemetrics,gainloss,sex,gender,metrics,segmetrics,bintest,import-picard,import-seg,import-theta,import-rna,export,version}
              Sub-commands (use with -h for more info)

       batch  Run the complete CNVkit pipeline on one or more BAM files.

       target Transform bait intervals into targets more suitable for CNVkit.

       access List the locations of accessible sequence regions in a FASTA file.

       antitarget
              Derive off-target ("antitarget") bins from target regions.

       autobin
              Quickly calculate reasonable bin sizes from BAM read counts.

       coverage
              Calculate coverage in the given regions from BAM read depths.

       reference
              Compile a coverage reference from the given files (normal samples).

       fix    Combine target and antitarget coverages and correct for biases. Adjust raw coverage
              data according to the given reference, correct potential biases and recenter.

       segment
              Infer copy number segments from the given coverage table.

       call   Call copy number variants from segmented log2 ratios.

       diagram
              Draw copy number (log2 coverages, segments) on chromosomes as a  diagram.  If  both
              the  raw  probes  and segments are given, show them side-by-side on each chromosome
              (segments on the left side, probes on the right side).

       scatter
              Plot probe log2 coverages and segmentation calls together.

       heatmap
              Plot copy number for multiple samples as a heatmap.

       breaks List the targeted genes in which a copy number breakpoint occurs.

       genemetrics
              Identify targeted genes with copy number gain or loss.

       sex    Guess samples' sex from the relative coverage of chromosomes X and Y.

       metrics
              Compute coverage deviations and other metrics for self-evaluation.

       segmetrics
              Compute segment-level metrics from bin-level log2 ratios.

       bintest
              Test for single-bin copy number alterations.

       import-picard
              Convert Picard CalculateHsMetrics tabular output to CNVkit .cnn  files.  The  input
              file  is  generated  by  the  PER_TARGET_COVERAGE  option in the CalculateHsMetrics
              script in Picard tools. If 'antitarget' is in the  input  filename,  the  generated
              output   filename   will   have  the  suffix  '.antitargetcoverage.cnn',  otherwise
              '.targetcoverage.cnn'.

       import-seg
              Convert a SEG file to CNVkit .cns files.

       import-theta
              Convert THetA output to a BED-like, CNVkit-like tabular format.  Equivalently,  use
              the  THetA  results  file  to  convert  CNVkit .cns segments to integer copy number
              calls.

       import-rna
              Convert a cohort of per-gene log2 ratios to CNVkit .cnr format.

       export Convert CNVkit output files to another format.

       version
              Display this program's version.

   optional arguments:
       -h, --help
              show this help message and exit

       See the online manual for details: https://cnvkit.readthedocs.io