.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.47.10.
.TH CNVKIT_SEGMENT "1" "March 2019" "cnvkit_segment 0.9.5" "User Commands"
.SH NAME
cnvkit_segment \- Infer copy number segments from the given coverage table.
.SH DESCRIPTION
usage: cnvkit segment [\-h] [\-o FILENAME] [\-d DATAFRAME]
.TP
[\-m {cbs,flasso,haar,none,hmm,hmm\-tumor,hmm\-germline}]
[\-t THRESHOLD] [\-\-drop\-low\-coverage]
[\-\-drop\-outliers FACTOR] [\-\-rscript\-path PATH]
[\-p [PROCESSES]] [\-v FILENAME] [\-i SAMPLE_ID]
[\-n NORMAL_ID] [\-\-min\-variant\-depth MIN_VARIANT_DEPTH]
[\-z [ALT_FREQ]]
filename
.SS "positional arguments:"
.TP
filename
Bin\-level log2 ratios (.cnr file), as produced by
\&'fix'.
.SS "optional arguments:"
.TP
\fB\-h\fR, \fB\-\-help\fR
show this help message and exit
.TP
\fB\-o\fR FILENAME, \fB\-\-output\fR FILENAME
Output table file name (CNR\-like table of segments,
\&.cns).
.TP
\fB\-d\fR DATAFRAME, \fB\-\-dataframe\fR DATAFRAME
File name to save the raw R dataframe emitted by CBS
or Fused Lasso. (Useful for debugging.)
.TP
\fB\-m\fR {cbs,flasso,haar,none,hmm,hmm\-tumor,hmm\-germline}, \fB\-\-method\fR {cbs,flasso,haar,none,hmm,hmm\-tumor,hmm\-germline}
Segmentation method (CBS, fused lasso, haar wavelet,
HMM), or 'none' for chromosome arm\-level averages as
segments. [Default: cbs]
.TP
\fB\-t\fR THRESHOLD, \fB\-\-threshold\fR THRESHOLD
Significance threshold (p\-value or FDR, depending on
method) to accept breakpoints during segmentation. For
HMM methods, this is the smoothing window size.
.TP
\fB\-\-drop\-low\-coverage\fR
Drop very\-low\-coverage bins before segmentation to
avoid false\-positive deletions in poor\-quality tumor
samples.
.TP
\fB\-\-drop\-outliers\fR FACTOR
Drop outlier bins more than this many multiples of the
95th quantile away from the average within a rolling
window. Set to 0 for no outlier filtering. [Default:
10]
.TP
\fB\-\-rscript\-path\fR PATH
Path to the Rscript executable to use for running R
code. Use this option to specify a non\-default R
installation. [Default: Rscript]
.TP
\fB\-p\fR [PROCESSES], \fB\-\-processes\fR [PROCESSES]
Number of subprocesses to segment in parallel. Give 0
or a negative value to use the maximum number of
available CPUs. [Default: use 1 process]
.SS "To additionally segment SNP b-allele frequencies:"
.TP
\fB\-v\fR FILENAME, \fB\-\-vcf\fR FILENAME
VCF file name containing variants for segmentation by
allele frequencies.
.TP
\fB\-i\fR SAMPLE_ID, \fB\-\-sample\-id\fR SAMPLE_ID
Specify the name of the sample in the VCF (\fB\-v\fR/\-\-vcf)
to use for b\-allele frequency extraction and as the
default plot title.
.TP
\fB\-n\fR NORMAL_ID, \fB\-\-normal\-id\fR NORMAL_ID
Corresponding normal sample ID in the input VCF
(\fB\-v\fR/\-\-vcf). This sample is used to select only
germline SNVs to plot b\-allele frequencies.
.TP
\fB\-\-min\-variant\-depth\fR MIN_VARIANT_DEPTH
Minimum read depth for a SNV to be displayed in the
b\-allele frequency plot. [Default: 20]
.TP
\fB\-z\fR [ALT_FREQ], \fB\-\-zygosity\-freq\fR [ALT_FREQ]
Ignore VCF's genotypes (GT field) and instead infer
zygosity from allele frequencies. [Default if used
without a number: 0.25]