.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.47.10.
.TH CNVKIT_REFERENCE "1" "March 2019" "cnvkit_reference 0.9.5" "User Commands"
.SH NAME
cnvkit_reference \- Compile a coverage reference from the given files (normal samples).
.SH DESCRIPTION
usage: cnvkit reference [\-h] [\-f FASTA] [\-o FILENAME] [\-y]
.TP
[\-x {m,y,male,Male,f,x,female,Female}] [\-t TARGETS]
[\-a ANTITARGETS] [\-\-no\-gc] [\-\-no\-edge] [\-\-no\-rmask]
[references [references ...]]
.SS "positional arguments:"
.TP
references
Normal\-sample target or antitarget .cnn files, or the
directory that contains them.
.SS "optional arguments:"
.TP
\fB\-h\fR, \fB\-\-help\fR
show this help message and exit
.TP
\fB\-f\fR FASTA, \fB\-\-fasta\fR FASTA
Reference genome, FASTA format (e.g. UCSC hg19.fa)
.TP
\fB\-o\fR FILENAME, \fB\-\-output\fR FILENAME
Output file name.
.TP
\fB\-y\fR, \fB\-\-male\-reference\fR, \fB\-\-haploid\-x\-reference\fR
Create a male reference: shift female samples' chrX
log\-coverage by \fB\-1\fR, so the reference chrX average is
\fB\-1\fR. Otherwise, shift male samples' chrX by +1, so the
reference chrX average is 0.
.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 chromosomal sex of all given samples as
male or female. (Default: guess each sample from
coverage of X and Y chromosomes).
.SS "To construct a generic, "flat" copy number reference with neutral expected coverage:"
.TP
\fB\-t\fR TARGETS, \fB\-\-targets\fR TARGETS
Target intervals (.bed or .list)
.TP
\fB\-a\fR ANTITARGETS, \fB\-\-antitargets\fR ANTITARGETS
Antitarget intervals (.bed or .list)
.SS "To disable specific automatic bias corrections:"
.TP
\fB\-\-no\-gc\fR
Skip GC correction.
.TP
\fB\-\-no\-edge\fR
Skip edge\-effect correction.
.TP
\fB\-\-no\-rmask\fR
Skip RepeatMasker correction.