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.
- {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.
- -h, --help
- show this help message and exit
See the online manual for details:
https://cnvkit.readthedocs.io