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'\" t
.TH samtools-flags 1 "12 September 2024" "samtools-1.21" "Bioinformatics tools"
.SH NAME
samtools flags \- convert between textual and numeric flag representation.
.\"
.\" Copyright (C) 2008-2011, 2013-2018 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.
.
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.SH SYNOPSIS
.PP
samtools flags
.IR FLAGS ...
.SH DESCRIPTION
.PP
Convert between textual and numeric flag representation.
Each \fIFLAGS\fP argument may be either an integer (in decimal, hexadecimal,
or octal) representing a combination of the listed numeric flag values,
or a comma-separated string \fINAME\fB,\fR...\fB,\fINAME\fR representing
a combination of the flag names listed below.
.B FLAGS:
.TS
rb l l .
0x1 PAIRED paired-end (or multiple-segment) sequencing technology
0x2 PROPER_PAIR each segment properly aligned according to the aligner
0x4 UNMAP segment unmapped
0x8 MUNMAP next segment in the template unmapped
0x10 REVERSE SEQ is reverse complemented
0x20 MREVERSE SEQ of the next segment in the template is reverse complemented
0x40 READ1 the first segment in the template
0x80 READ2 the last segment in the template
0x100 SECONDARY secondary alignment
0x200 QCFAIL not passing quality controls
0x400 DUP PCR or optical duplicate
0x800 SUPPLEMENTARY supplementary alignment
.TE
.SH AUTHOR
.PP
Written by Petr Danacek from the Sanger Institute.
.SH SEE ALSO
.IR samtools (1)
.PP
Samtools website: <http://www.htslib.org/>
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