.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.49.3.
.TH CNVKIT_COVERAGE "1" "July 2023" "cnvkit.py coverage 0.9.10" "User Commands"
.SH NAME
cnvkit_coverage \- Calculate coverage in the given regions from BAM read depths.
.SH DESCRIPTION
usage: cnvkit.py coverage [\-h] [\-f FILENAME] [\-c] [\-q MIN_MAPQ] [\-o FILENAME]
.TP
[\-p [PROCESSES]]
bam_file interval
.SS "positional arguments:"
.TP
bam_file
Mapped sequence reads (.bam)
.TP
interval
Intervals (.bed or .list)
.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\-c\fR, \fB\-\-count\fR
Get read depths by counting read midpoints within each
bin. (An alternative algorithm).
.TP
\fB\-q\fR MIN_MAPQ, \fB\-\-min\-mapq\fR MIN_MAPQ
Minimum mapping quality score (phred scale 0\-60) to
count a read for coverage depth. [Default: 0]
.TP
\fB\-o\fR FILENAME, \fB\-\-output\fR FILENAME
Output file name.
.TP
\fB\-p\fR [PROCESSES], \fB\-\-processes\fR [PROCESSES]
Number of subprocesses to calculate coverage in
parallel. Without an argument, use the maximum number
of available CPUs. [Default: use 1 process]