.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.47.10.
.TH CNVKIT "1" "March 2019" "cnvkit 0.9.5" "User Commands"
.SH NAME
cnvkit \- a command-line toolkit for copy number analysis.
.SH DESCRIPTION
usage: cnvkit [\-h]
.IP
{batch,target,access,antitarget,autobin,coverage,reference,fix,segment,call,diagram,scatter,heatmap,breaks,genemetrics,gainloss,sex,gender,metrics,segmetrics,import\-picard,import\-seg,import\-theta,import\-rna,export,version}
\&...
.PP
CNVkit, a command\-line toolkit for copy number analysis.
.SS "positional arguments:"
.TP
{batch,target,access,antitarget,autobin,coverage,reference,fix,segment,call,diagram,scatter,heatmap,breaks,genemetrics,gainloss,sex,gender,metrics,segmetrics,import\-picard,import\-seg,import\-theta,import\-rna,export,version}
Sub\-commands (use with \fB\-h\fR for more info)
.TP
batch
Run the complete CNVkit pipeline on one or more BAM
files.
.TP
target
Transform bait intervals into targets more suitable
for CNVkit.
.TP
access
List the locations of accessible sequence regions in a
FASTA file.
.TP
antitarget
Derive off\-target ("antitarget") bins from target
regions.
.TP
autobin
Quickly calculate reasonable bin sizes from BAM read
counts.
.TP
coverage
Calculate coverage in the given regions from BAM read
depths.
.TP
reference
Compile a coverage reference from the given files
(normal samples).
.TP
fix
Combine target and antitarget coverages and correct
for biases. Adjust raw coverage data according to the
given reference, correct potential biases and recenter.
.TP
segment
Infer copy number segments from the given coverage
table.
.TP
call
Call copy number variants from segmented log2 ratios.
.TP
diagram
Draw copy number (log2 coverages, CBS calls) 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).
.TP
scatter
Plot probe log2 coverages and segmentation calls
together.
.TP
heatmap
Plot copy number for multiple samples as a heatmap.
.TP
breaks
List the targeted genes in which a copy number
breakpoint occurs.
.TP
genemetrics
Identify targeted genes with copy number gain or loss.
.TP
sex
Guess samples' sex from the relative coverage of
chromosomes X and Y.
.TP
metrics
Compute coverage deviations and other metrics for
self\-evaluation.
.TP
segmetrics
Compute segment\-level metrics from bin\-level log2
ratios.
.TP
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'.
.TP
import\-seg
Convert a SEG file to CNVkit .cns files.
.TP
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.
.TP
import\-rna
Convert a cohort of per\-gene log2 ratios to CNVkit
\&.cnr format.
.TP
export
Convert CNVkit output files to another format.
.TP
version
Display this program's version.
.SS "optional arguments:"
.TP
\fB\-h\fR, \fB\-\-help\fR
show this help message and exit
.PP
See the online manual for details: https://cnvkit.readthedocs.io