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'\" t
.TH samtools-bedcov 1 "12 September 2024" "samtools-1.21" "Bioinformatics tools"
.SH NAME
samtools bedcov \- reports coverage over regions in a supplied BED file
.\"
.\" Copyright (C) 2008-2011, 2013-2018, 2020, 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)
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.SH SYNOPSIS
.PP
samtools bedcov
.RI [ options ]
.IR region.bed " " in1.sam | in1.bam | in1.cram "[...]"
.SH DESCRIPTION
.PP
Reports the total read base count (i.e. the sum of per base read depths)
for each genomic region specified in the supplied BED file. The regions
are output as they appear in the BED file and are 0-based.
Columns 1-3 are chrom/start/end as per the input BED file, followed by N
columns of coverages (for N input BAMs), then (if given -d), N columns of
bases-at-depth-X, then (if given -c) N columns of read counts.
.SH OPTIONS
.TP
.BI "-Q,\ --min-MQ " INT
.RI "Only count reads with mapping quality greater than or equal to " INT
.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
Discard any read that has any of the flags specified by
.I FLAGS
set. FLAGS are specified as for the
.B "-g"
option. [UNMAP,SECONDARY,QCFAIL,DUP]
.TP
.B -j
Do not include deletions (D) and ref skips (N) in bedcov computation.
.TP
.BI "-d " INT
Print an additional column, for each file, containing the number of bases having
a depth above and including the given threshold. If the option is not used, the
extra column is not displayed. The option value must be an integer >= 0.
.TP
.BI "--max-depth " INT
Specifies the maximum depth used for the mpileup algorithm.
If \fB-d\fR is used and is larger then this value will be used instead.
Defaults to 2 billion, but smaller values may be used when we do not
require an exact count in excessively deep regions and are interested
in maximising speed of results.
.TP
.B -c
Print an additional column with the read count for this region. This
will be +1 for every read covering the region, not just starting
within in. The whole read filtering options \fB-Q\fR, \fB-g\fR and
\fB-G\fR options will also have an affect on this count, but \fB-d\fR
will not.
.TP
.B "-X"
If this option is set, it will allows user to specify customized index file location(s) if the data
folder does not contain any index file. Example usage: samtools bedcov [options] -X <in.bed> </data_folder/in1.bam> [...] </index_folder/index1.bai> [...]
.TP
.B "-H"
.RI "print a comment/header describing columns"
.SH AUTHOR
.PP
Written by Heng Li from the Sanger Institute.
.SH SEE ALSO
.IR samtools (1)
.PP
Samtools website: <http://www.htslib.org/>
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