CNVKIT.PY(1)

NAME
cnvkit.py - Copy number variant detection from targeted DNA sequencing

DESCRIPTION
usage: cnvkit.py [-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.

  options:

-h, --help
    show this help message and exit

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

AUTHOR
 This manpage was written by Andreas Tille for the Debian distribution and
 can be used for any other usage of the program.