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samtools-dict.1
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'\" t
.TH samtools-dict 1 "2 September 2022" "samtools-1.16.1" "Bioinformatics tools"
.SH NAME
samtools dict \- create a sequence dictionary file from a fasta file
.\"
.\" 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.
.
.\" For code blocks and examples (cf groff's Ultrix-specific man macros)
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.SH SYNOPSIS
.PP
samtools dict
.IR ref.fasta | ref.fasta.gz
.SH DESCRIPTION
.PP
Create a sequence dictionary file from a fasta file.
.SH OPTIONS
.TP 11
.BI -a,\ --assembly \ STR
Specify the assembly for the AS tag.
.TP
.B -A, --alias, --alternative-name
Add an AN tag with the same value as the SN tag, except that a \(lqchr\(rq
prefix is removed if SN has one or added if it does not.
For mitochondria (i.e., when SN is \(lqM\(rq or \(lqMT\(rq, with or without a
\(lqchr\(rq prefix), also adds the remaining combinations of \(lqchr/M/MT\(rq
to the AN tag.
.TP
.B -H,\ --no-header
Do not print the @HD header line.
.TP
.BI "-l, --alt " FILE
Add an AH tag to each sequence listed in the specified
.IR bwa (1)-style
.B .alt
file.
These files use SAM records to represent alternate locus sequences
(as named in the
.B QNAME
field) and their mappings to the primary assembly.
.TP
.BI -o,\ --output \ FILE
Output to
.I FILE
[stdout].
.TP
.BI -s,\ --species \ STR
Specify the species for the SP tag.
.TP
.BI -u,\ --uri \ STR
Specify the URI for the UR tag. Defaults to
the absolute path of
.I ref.fasta
unless reading from stdin.
.SH AUTHOR
.PP
Written by Shane McCarthy from the Sanger Institute.
.SH SEE ALSO
.IR samtools (1),
.IR bcftools (1),
.IR bwa (1),
.IR sam (5),
.IR tabix (1)
.PP
Samtools website: <http://www.htslib.org/>
.br
File format specification of SAM/BAM,CRAM,VCF/BCF: <http://samtools.github.io/hts-specs>
.br
Samtools latest source: <https://github.com/samtools/samtools>
.br
HTSlib latest source: <https://github.com/samtools/htslib>
.br
Bcftools website: <http://samtools.github.io/bcftools>