.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.49.2.
.TH MOSDEPTH "1" "November 2022" "mosdepth 0.3.3" "User Commands"
.SH NAME
mosdepth \- manual page for mosdepth 0.3.3
.SH DESCRIPTION
mosdepth 0.3.3
.IP
Usage: mosdepth [options] <prefix> <BAM\-or\-CRAM>
.PP
Arguments:
.TP
<prefix>
outputs: `{prefix}.mosdepth.dist.txt`
.TP
`{prefix}.mosdepth.summary.txt`
`{prefix}.per\-base.bed.gz` (unless \fB\-n\fR/\-\-no\-per\-base is specified)
`{prefix}.regions.bed.gz` (if \fB\-\-by\fR is specified)
`{prefix}.quantized.bed.gz` (if \fB\-\-quantize\fR is specified)
`{prefix}.thresholds.bed.gz` (if \fB\-\-thresholds\fR is specified)
.TP
<BAM\-or\-CRAM>
the alignment file for which to calculate depth.
.PP
Common Options:
.TP
\fB\-t\fR \fB\-\-threads\fR <threads>
number of BAM decompression threads [default: 0]
.TP
\fB\-c\fR \fB\-\-chrom\fR <chrom>
chromosome to restrict depth calculation.
.TP
\fB\-b\fR \fB\-\-by\fR <bed|window>
optional BED file or (integer) window\-sizes.
.TP
\fB\-n\fR \fB\-\-no\-per\-base\fR
dont output per\-base depth. skipping this output will speed execution
substantially. prefer quantized or thresholded values if possible.
.TP
\fB\-f\fR \fB\-\-fasta\fR <fasta>
fasta file for use with CRAM files [default: ].
.PP
Other options:
.TP
\fB\-F\fR \fB\-\-flag\fR <FLAG>
exclude reads with any of the bits in FLAG set [default: 1796]
.TP
\fB\-i\fR \fB\-\-include\-flag\fR <FLAG>
only include reads with any of the bits in FLAG set. default is unset. [default: 0]
.TP
\fB\-x\fR \fB\-\-fast\-mode\fR
dont look at internal cigar operations or correct mate overlaps (recommended for most use\-cases).
.TP
\fB\-q\fR \fB\-\-quantize\fR <segments>
write quantized output see docs for description.
.TP
\fB\-Q\fR \fB\-\-mapq\fR <mapq>
mapping quality threshold. reads with a quality less than this value are ignored [default: 0]
.TP
\fB\-T\fR \fB\-\-thresholds\fR <thresholds>
for each interval in \fB\-\-by\fR, write number of bases covered by at
least threshold bases. Specify multiple integer values separated
by ','.
.TP
\fB\-m\fR \fB\-\-use\-median\fR
output median of each region (in \fB\-\-by\fR) instead of mean.
.TP
\fB\-R\fR \fB\-\-read\-groups\fR <string>
only calculate depth for these comma\-separated read groups IDs.
.TP
\fB\-h\fR \fB\-\-help\fR
show help