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