.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.47.16.
.TH CNVKIT_CALL "1" "January 2021" "cnvkit call 0.9.8" "User Commands"
.SH NAME
cnvkit_call \- Call copy number variants from segmented log2 ratios.
.SH DESCRIPTION
usage: cnvkit call [\-h] [\-\-center [{mean,median,mode,biweight}]]
.IP
[\-\-center\-at CENTER_AT] [\-\-filter {ampdel,cn,ci,sem}]
[\-m {threshold,clonal,none}] [\-t THRESHOLDS]
[\-\-ploidy PLOIDY] [\-\-purity PURITY] [\-\-drop\-low\-coverage]
[\-x {m,y,male,Male,f,x,female,Female}] [\-y] [\-o FILENAME]
[\-v FILENAME] [\-i SAMPLE_ID] [\-n NORMAL_ID]
[\-\-min\-variant\-depth MIN_VARIANT_DEPTH] [\-z [ALT_FREQ]]
filename
.SS "positional arguments:"
.TP
filename
Copy ratios (.cnr or .cns).
.SS "optional arguments:"
.TP
\fB\-h\fR, \fB\-\-help\fR
show this help message and exit
.TP
\fB\-\-center\fR [{mean,median,mode,biweight}]
Re\-center the log2 ratio values using this estimator
of the center or average value. ('median' if no
argument given.)
.TP
\fB\-\-center\-at\fR CENTER_AT
Subtract a constant number from all log2 ratios. For
"manual" re\-centering, in case the \fB\-\-center\fR option
gives unsatisfactory results.)
.TP
\fB\-\-filter\fR {ampdel,cn,ci,sem}
Merge segments flagged by the specified filter(s) with
the adjacent segment(s).
.TP
\fB\-m\fR {threshold,clonal,none}, \fB\-\-method\fR {threshold,clonal,none}
Calling method. [Default: threshold]
.TP
\fB\-t\fR THRESHOLDS, \fB\-\-thresholds\fR THRESHOLDS
Hard thresholds for calling each integer copy number,
separated by commas. Use the '=' sign on the command
line, e.g.: \fB\-t\fR=\fI\,\-1\/\fR,0,1 [Default: \fB\-1\fR.1,\-0.25,0.2,0.7]
.TP
\fB\-\-ploidy\fR PLOIDY
Ploidy of the sample cells. [Default: 2]
.TP
\fB\-\-purity\fR PURITY
Estimated tumor cell fraction, a.k.a. purity or
cellularity.
.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\-x\fR {m,y,male,Male,f,x,female,Female}, \fB\-\-sample\-sex\fR {m,y,male,Male,f,x,female,Female}, \fB\-g\fR {m,y,male,Male,f,x,female,Female}, \fB\-\-gender\fR {m,y,male,Male,f,x,female,Female}
Specify the sample's chromosomal sex as male or
female. (Otherwise guessed from X and Y coverage).
.TP
\fB\-y\fR, \fB\-\-male\-reference\fR, \fB\-\-haploid\-x\-reference\fR
Was a male reference used? If so, expect half ploidy
on chrX and chrY; otherwise, only chrY has half
ploidy. In CNVkit, if a male reference was used, the
"neutral" copy number (ploidy) of chrX is 1; chrY is
haploid for either reference sex.
.TP
\fB\-o\fR FILENAME, \fB\-\-output\fR FILENAME
Output table file name (CNR\-like table of segments,
\&.cns).
.SS "To additionally process SNP b-allele frequencies for allelic copy number:"
.TP
\fB\-v\fR FILENAME, \fB\-\-vcf\fR FILENAME
VCF file name containing variants for calculation of
b\-allele frequencies.
.TP
\fB\-i\fR SAMPLE_ID, \fB\-\-sample\-id\fR SAMPLE_ID
Name of the sample in the VCF (\fB\-v\fR/\-\-vcf) to use for
b\-allele frequency extraction.
.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 calculate b\-allele frequencies.
.TP
\fB\-\-min\-variant\-depth\fR MIN_VARIANT_DEPTH
Minimum read depth for a SNV to be used in the
b\-allele frequency calculation. [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]