.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.47.10.
.TH CNVKIT_BATCH "1" "March 2019" "cnvkit_batch 0.9.5" "User Commands"
.SH NAME
cnvkit_batch \- Run the complete CNVkit pipeline on one or more BAM files.
.SH DESCRIPTION
usage: cnvkit batch [\-h] [\-m {hybrid,amplicon,wgs}] [\-y] [\-c]
.TP
[\-\-drop\-low\-coverage] [\-p [PROCESSES]]
[\-\-rscript\-path PATH] [\-n [FILES [FILES ...]]]
[\-f FILENAME] [\-t FILENAME] [\-a FILENAME]
[\-\-annotate FILENAME] [\-\-short\-names]
[\-\-target\-avg\-size TARGET_AVG_SIZE] [\-g FILENAME]
[\-\-antitarget\-avg\-size ANTITARGET_AVG_SIZE]
[\-\-antitarget\-min\-size ANTITARGET_MIN_SIZE]
[\-\-output\-reference FILENAME] [\-r REFERENCE]
[\-d DIRECTORY] [\-\-scatter] [\-\-diagram]
[bam_files [bam_files ...]]
.SS "positional arguments:"
.TP
bam_files
Mapped sequence reads (.bam)
.SS "optional arguments:"
.TP
\fB\-h\fR, \fB\-\-help\fR
show this help message and exit
.TP
\fB\-m\fR {hybrid,amplicon,wgs}, \fB\-\-method\fR {hybrid,amplicon,wgs}
Sequencing protocol: hybridization capture ('hybrid'),
targeted amplicon sequencing ('amplicon'), or whole
genome sequencing ('wgs'). Determines whether and how
to use antitarget bins. [Default: hybrid]
.TP
\fB\-y\fR, \fB\-\-male\-reference\fR, \fB\-\-haploid\-x\-reference\fR
Use or assume a male reference (i.e. female samples
will have +1 log\-CNR of chrX; otherwise male samples
would have \fB\-1\fR chrX).
.TP
\fB\-c\fR, \fB\-\-count\-reads\fR
Get read depths by counting read midpoints within each
bin. (An alternative algorithm).
.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\-p\fR [PROCESSES], \fB\-\-processes\fR [PROCESSES]
Number of subprocesses used to running each of the BAM
files in parallel. Without an argument, use the
maximum number of available CPUs. [Default: process
each BAM in serial]
.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]
.SS "To construct a new copy number reference:"
.TP
\fB\-n\fR [FILES [FILES ...]], \fB\-\-normal\fR [FILES [FILES ...]]
Normal samples (.bam) used to construct the pooled,
paired, or flat reference. If this option is used but
no filenames are given, a "flat" reference will be
built. Otherwise, all filenames following this option
will be used.
.TP
\fB\-f\fR FILENAME, \fB\-\-fasta\fR FILENAME
Reference genome, FASTA format (e.g. UCSC hg19.fa)
.TP
\fB\-t\fR FILENAME, \fB\-\-targets\fR FILENAME
Target intervals (.bed or .list)
.TP
\fB\-a\fR FILENAME, \fB\-\-antitargets\fR FILENAME
Antitarget intervals (.bed or .list)
.TP
\fB\-\-annotate\fR FILENAME
Use gene models from this file to assign names to the
target regions. Format: UCSC refFlat.txt or
ensFlat.txt file (preferred), or BED, interval list,
GFF, or similar.
.TP
\fB\-\-short\-names\fR
Reduce multi\-accession bait labels to be short and
consistent.
.TP
\fB\-\-target\-avg\-size\fR TARGET_AVG_SIZE
Average size of split target bins (results are
approximate).
.TP
\fB\-g\fR FILENAME, \fB\-\-access\fR FILENAME
Regions of accessible sequence on chromosomes (.bed),
as output by the 'access' command.
.TP
\fB\-\-antitarget\-avg\-size\fR ANTITARGET_AVG_SIZE
Average size of antitarget bins (results are
approximate).
.TP
\fB\-\-antitarget\-min\-size\fR ANTITARGET_MIN_SIZE
Minimum size of antitarget bins (smaller regions are
dropped).
.TP
\fB\-\-output\-reference\fR FILENAME
Output filename/path for the new reference file being
created. (If given, ignores the \fB\-o\fR/\-\-output\-dir option
and will write the file to the given path. Otherwise,
"reference.cnn" will be created in the current
directory or specified output directory.)
.SS "To reuse an existing reference:"
.TP
\fB\-r\fR REFERENCE, \fB\-\-reference\fR REFERENCE
Copy number reference file (.cnn).
.SS "Output options:"
.TP
\fB\-d\fR DIRECTORY, \fB\-\-output\-dir\fR DIRECTORY
Output directory.
.TP
\fB\-\-scatter\fR
Create a whole\-genome copy ratio profile as a PDF
scatter plot.
.TP
\fB\-\-diagram\fR
Create an ideogram of copy ratios on chromosomes as a
PDF.