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'\" t
.TH samtools-index 1 "12 September 2024" "samtools-1.21" "Bioinformatics tools"
.SH NAME
samtools index \- indexes SAM/BAM/CRAM files
.\"
.\" Copyright (C) 2008-2011, 2013-2020 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
. in +\\$1
. nf
. ft CR
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.de EE
. ft
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. in
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.SH SYNOPSIS
.PP
.B samtools index -M
.RB [ -bc ]
.RB [ -m
.IR INT ]
.I FILE FILE
.RI [ FILE ...]
.PP
.B samtools index
.RB [ -bc ]
.RB [ -m
.IR INT ]
.IR aln.sam | aln.bam | aln.cram
.RI [ out.index ]
.SH DESCRIPTION
.PP
Index coordinate-sorted BGZIP-compressed SAM, BAM or CRAM files for fast
random access.
Note for SAM this only works if the file has been BGZF compressed first.
(The first synopsis with multiple input
.IR FILE s
is only available with Samtools 1.16 or later.)
This index is needed when
.I region
arguments are used to limit
.B samtools view
and similar commands to particular regions of interest.
When only one alignment file is being indexed, the output index filename
can be specified via
.B -o
or as shown in the second synopsis.
When no output filename is specified, for a CRAM file
.IR aln.cram ,
index file
.IB aln.cram .crai
will be created; for a BAM file
.IR aln.bam ,
either
.IB aln.bam .bai
or
.IB aln.bam .csi
will be created; and for a compressed SAM file
.IR aln.sam.gz ,
either
.IB aln.sam.gz .bai
or
.IB aln.sam.gz .csi
will be created, depending on the index format selected.
The BAI index format can handle individual chromosomes up to 512 Mbp
(2^29 bases) in length.
If your input file might contain reads mapped to positions greater than that,
you will need to use a CSI index.
.SH OPTIONS
.TP 8
.B -b, --bai
Create a BAI index.
This is currently the default when no format options are used.
.TP
.B -c, --csi
Create a CSI index.
By default, the minimum interval size for the index is 2^14, which is the same
as the fixed value used by the BAI format.
.TP
.BI "-m, --min-shift " INT
Create a CSI index, with a minimum interval size of 2^INT.
.TP
.B -M
Interpret all filename arguments as alignment files to be indexed individually.
(Without
.BR -M ,
filename arguments are interpreted solely as per the second synopsis.)
.TP
.BI "-o, --output " FILE
Write the output index to
.IR FILE .
(Currently may only be used when exactly one alignment file is being indexed.)
.TP
.BI "-@, --threads " INT
Number of input/output compression threads to use in addition to main thread [0].
.SH AUTHOR
.PP
Written by Heng Li from the Sanger Institute.
.SH SEE ALSO
.IR samtools (1),
.IR samtools-idxstats (1),
.IR samtools-view (1)
.PP
Samtools website: <http://www.htslib.org/>
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