'\" t .TH samtools-bedcov 1 "24 January 2024" "samtools-1.19.2" "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 .\" Author: Joshua C. Randall .\" .\" 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 . in +\\$1 . nf . ft CR .. .de EE . ft . fi . in .. . .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. Counts for each alignment file supplied are reported in separate columns. .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 .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 [...] [...] .SH AUTHOR .PP Written by Heng Li from the Sanger Institute. .SH SEE ALSO .IR samtools (1) .PP Samtools website: