.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.49.2.
.TH CNVKIT_AUTOBIN "1" "September 2022" "cnvkit autobin 0.9.9" "User Commands"
.SH NAME
cnvkit_autobin \- Quickly calculate reasonable bin sizes from BAM read counts.
.SH DESCRIPTION
usage: cnvkit autobin [\-h] [\-f FILENAME] [\-m {hybrid,amplicon,wgs}]
.TP
[\-g FILENAME] [\-t TARGETS] [\-b BP_PER_BIN]
[\-\-target\-max\-size BASES] [\-\-target\-min\-size BASES]
[\-\-antitarget\-max\-size BASES]
[\-\-antitarget\-min\-size BASES] [\-\-annotate FILENAME]
[\-\-short\-names] [\-\-target\-output\-bed FILENAME]
[\-\-antitarget\-output\-bed FILENAME]
bams [bams ...]
.SS "positional arguments:"
.TP
bams
Sample BAM file(s) to test for target coverage
.SS "options:"
.TP
\fB\-h\fR, \fB\-\-help\fR
show this help message and exit
.TP
\fB\-f\fR FILENAME, \fB\-\-fasta\fR FILENAME
Reference genome, FASTA format (e.g. UCSC hg19.fa)
.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\-g\fR FILENAME, \fB\-\-access\fR FILENAME
Sequencing\-accessible genomic regions, or exons to use
as possible targets (e.g. output of refFlat2bed.py)
.TP
\fB\-t\fR TARGETS, \fB\-\-targets\fR TARGETS
Potentially targeted genomic regions, e.g. all
possible exons for the reference genome. Format: BED,
interval list, etc.
.TP
\fB\-b\fR BP_PER_BIN, \fB\-\-bp\-per\-bin\fR BP_PER_BIN
Desired average number of sequencing read bases mapped
to each bin. [Default: 100000.0]
.TP
\fB\-\-target\-max\-size\fR BASES
Maximum size of target bins. [Default: 20000]
.TP
\fB\-\-target\-min\-size\fR BASES
Minimum size of target bins. [Default: 20]
.TP
\fB\-\-antitarget\-max\-size\fR BASES
Maximum size of antitarget bins. [Default: 500000]
.TP
\fB\-\-antitarget\-min\-size\fR BASES
Minimum size of antitarget bins. [Default: 500]
.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\-output\-bed\fR FILENAME
Filename for target BED output. If not specified,
constructed from the input file basename.
.TP
\fB\-\-antitarget\-output\-bed\fR FILENAME
Filename for antitarget BED output. If not specified,
constructed from the input file basename.