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'\" t
.TH samtools-depth 1 "12 September 2024" "samtools-1.21" "Bioinformatics tools"
.SH NAME
samtools depth \- computes the read depth at each position or region
.\"
.\" Copyright (C) 2008-2011, 2013-2022 Genome Research Ltd.
.\" Portions copyright (C) 2010, 2011 Broad Institute.
.\"
.\" Author: Heng Li <lh3@sanger.ac.uk>
.\" Author: Joshua C. Randall <jcrandall@alum.mit.edu>
.\"
.\" Permission is hereby granted, free of charge, to any person obtaining a
.\" copy of this software and associated documentation files (the "Software"),
.\" to deal in the Software without restriction, including without limitation
.\" the rights to use, copy, modify, merge, publish, distribute, sublicense,
.\" and/or sell copies of the Software, and to permit persons to whom the
.\" Software is furnished to do so, subject to the following conditions:
.\"
.\" The above copyright notice and this permission notice shall be included in
.\" all copies or substantial portions of the Software.
.\"
.\" THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
.\" IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
.\" FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL
.\" THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
.\" LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
.\" FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
.\" DEALINGS IN THE SOFTWARE.
.
.\" For code blocks and examples (cf groff's Ultrix-specific man macros)
.de EX
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.de EE
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.SH SYNOPSIS
.PP
samtools depth
.RI [ options ]
.RI "[" in1.sam | in1.bam | in1.cram " [" in2.sam | in2.bam | in2.cram "] [...]]"
.SH DESCRIPTION
.PP
Computes the depth at each position or region.
.SH OPTIONS
.TP 8
.B -a
Output all positions (including those with zero depth)
.TP
.B -a -a, -aa
Output absolutely all positions, including unused reference sequences.
Note that when used in conjunction with a BED file the -a option may
sometimes operate as if -aa was specified if the reference sequence
has coverage outside of the region specified in the BED file.
.TP
.BI "-b " FILE
.RI "Compute depth at list of positions or regions in specified BED " FILE.
[]
.TP
.BI "-f " FILE
.RI "Use the BAM files specified in the " FILE
(a file of filenames, one file per line)
[]
.TP
.B -H
Write a comment line showing column names at the beginning of the output.
The names are CHROM, POS, and then the input file name for each depth column.
If one of the inputs came from stdin, the name \*(lq-\*(rq will be used for
the corresponding column.
.TP
.BI "-l " INT
.RI "Ignore reads shorter than " INT "."
This is the number of bases in the sequence, minus any soft clips.
.TP
.BI "-m, -d " INT
(Deprecated since 1.13) This option previously limited the depth to a maximum
value. It is still accepted as an option, but ignored.
Note for single files, the behaviour of old
.B samtools depth -J -q0 -d
.I INT FILE
is identical to
.B samtools mpileup -A -Q0 -x -d
.I INT FILE
.B | cut -f 1,2,4
.TP
.BI "-o " FILE
.RI "Write output to " FILE ". Using \*(lq-\*(rq for " FILE
will send the output to stdout (also the default if this option is not used).
.TP
.BI "-q,\ --min-BQ " INT
.RI "Only count reads with base quality greater than or equal to " INT
.TP
.BI "-Q,\ --min-MQ " INT
.RI "Only count reads with mapping quality greater than or equal to " INT
.TP
.BI "-r " CHR ":" FROM "-" TO
Only report depth in specified region.
.TP
.B "-X"
If this option is set, it will allow the user to specify customized index file location(s) if the data
folder does not contain any index file. Example usage: samtools depth [options] -X /data_folder/in1.bam [/data_folder/in2.bam [...]] /index_folder/index1.bai [/index_folder/index2.bai [...]]
.TP
.BI "-g " FLAGS
By default, reads that have any of the flags UNMAP, SECONDARY, QCFAIL,
or DUP set are skipped. To include these reads back in the analysis, use
this option together with the desired flag or flag combination.
.I FLAGS
can be specified in hex by beginning with `0x' (i.e. /^0x[0-9A-F]+/),
in octal by beginning with `0' (i.e. /^0[0-7]+/), as a decimal number
not beginning with '0' or as a comma-separated list of flag names. [0]
For a list of flag names see
.IR samtools-flags (1).
.TP
.BI "-G " FLAGS ", --excl-flags " FLAGS
Discard reads that have any of the flags specified by
.I FLAGS
set. FLAGS are specified as for the
.B "-g"
option. [UNMAP,SECONDARY,QCFAIL,DUP]
.TP
.BI "--incl-flags " FLAGS
Only include reads with at least one bit set in
.I FLAGS
present in the FLAG field.
FLAGS are specified as for the
.B "-g"
option. [0]
.TP
.BI "--require-flags " FLAGS
Only include reads with all bits set in
.I FLAGS
present in the FLAG field.
FLAGS are specified as for the
.B "-g"
option. [0]
.TP
.B -J
Include reads with deletions in depth computation.
.TP
.B -s
For the overlapping section of a read pair, count only the bases of
the first read. Note this algorithm changed in 1.13 so the
results may differ slightly to older releases.
.SH CAVEATS
It may appear that "samtools depth" is simply "samtools mpileup" with some
of the columns removed, and indeed earlier versions of this command
were just this. However both then and now there are subtle
differences in parameters which make the two not entirely comparable.
Differences, other than the obvious speed benefits, include:
.IP o 2
Deletions (CIGAR element "D") are ignored by default in "depth". These
may be counted by adding the \fB-J\fR option. "Mpileup" always counts
the deleted bases, and has no option to toggle this.
.IP o 2
Beware there are idiosyncrasies in option naming. Specifically
\fB-q\fR and \fB-Q\fR options have their meanings swapped between
"depth" and "mpileup".
.IP o 2
The removal of overlapping sequences (option \fB-s\fR) is on by
default in "mpileup" and off by default in "depth". Additionally the
overlap removal algorithm differs, giving subtle changes when Ns are
present in the sequence. Also any paired read is considered for overlap
removal by "depth", rather than only those with the properly-paired flag
set ("mpileup"). See above for a more detailed description.
.IP o 2
The default minimum quality value is 0 for "depth" and 13 for "mpileup".
.IP o 2
Specifying multiple BAMs will produce one depth column per file with
"depth", but these are merged in "mpileup".
.IP o 2
"Depth" doesn't have a maximum depth limit, while "mpileup" defaults
to a maximum of 8000.
.IP o 2
If a reference is specified to "mpileup" the BAQ algorithm will be
used to adjust quality values, although it can be disabled. "Depth"
never uses BAQ.
.EE
.SH AUTHOR
.PP
Written by Heng Li and James Bonfield from the Sanger Institute.
.SH SEE ALSO
.IR samtools (1),
.IR samtools-mpileup (1),
.IR samtools-coverage (1),
.IR samtools-sort (1)
.PP
Samtools website: <http://www.htslib.org/>
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