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CNVKIT(1) User Commands CNVKIT(1)


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


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:

Sub-commands (use with -h for more info)
Run the complete CNVkit pipeline on one or more BAM files.
Transform bait intervals into targets more suitable for CNVkit.
List the locations of accessible sequence regions in a FASTA file.
Derive off-target ("antitarget") bins from target regions.
Quickly calculate reasonable bin sizes from BAM read counts.
Calculate coverage in the given regions from BAM read depths.
Compile a coverage reference from the given files (normal samples).
Combine target and antitarget coverages and correct for biases. Adjust raw coverage data according to the given reference, correct potential biases and recenter.
Infer copy number segments from the given coverage table.
Call copy number variants from segmented log2 ratios.
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).
Plot probe log2 coverages and segmentation calls together.
Plot copy number for multiple samples as a heatmap.
List the targeted genes in which a copy number breakpoint occurs.
Identify targeted genes with copy number gain or loss.
Guess samples' sex from the relative coverage of chromosomes X and Y.
Compute coverage deviations and other metrics for self-evaluation.
Compute segment-level metrics from bin-level log2 ratios.
Test for single-bin copy number alterations.
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'.
Convert a SEG file to CNVkit .cns files.
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.
Convert a cohort of per-gene log2 ratios to CNVkit .cnr format.
Convert CNVkit output files to another format.
Display this program's version.


show this help message and exit

See the online manual for details:

September 2022 cnvkit 0.9.9