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'\" t
.TH samtools-idxstats 1 "14 July 2025" "samtools-1.22.1" "Bioinformatics tools"
.SH NAME
samtools idxstats \- reports alignment summary statistics
.\"
.\" Copyright (C) 2008-2011, 2013-2018, 2024 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 idxstats
.IR in.sam | in.bam | in.cram
.SH DESCRIPTION
.PP
Retrieve and print stats in the index file corresponding to the input file.
Before calling idxstats, the input BAM file should be indexed by samtools index.
If run on a SAM or CRAM file or an unindexed BAM file, this command
will still produce the same summary statistics, but does so by reading
through the entire file. This is far slower than using the BAM
indices.
The output is TAB-delimited with each line consisting of reference sequence
name, sequence length, # mapped read-segments and # unmapped
read-segments. It is written to stdout. Note this may count reads
multiple times if they are mapped more than once or in multiple fragments.
.SH OPTIONS
.TP 11
.B -X
This option will allow the user to specify a customised index file
location. e.g.
.B samtools idxstat [options] -X /data_folder/data.bam /index_folder/index.bai
.SH AUTHOR
.PP
Written by Heng Li from the Sanger Institute.
.SH SEE ALSO
.IR samtools (1),
.IR samtools-flagstat (1),
.IR samtools-index (1),
.IR samtools-stats (1)
.PP
Samtools website: <http://www.htslib.org/>
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