---
name: "samtools-dict"
section: "1"
platform: "linux"
package: "samtools"
version: "1.21-1"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/samtools-dict"
---

# samtools-dict(1)

create a sequence dictionary file from a fasta file

## NAME

samtools-dict - create a sequence dictionary file from a fasta file

## SYNOPSIS

samtools dict *ref.fasta*\|*ref.fasta.gz*

## DESCRIPTION

Create a sequence dictionary file from a fasta file.

## OPTIONS

- **-a, --assembly** *STR*

  Specify the assembly for the AS tag.

- **-A, --alias, --alternative-name**

  Add an AN tag with the same value as the SN tag, except that a “chr” prefix is removed if SN has one or added if it does not. For mitochondria (i.e., when SN is “M” or “MT”, with or without a “chr” prefix), also adds the remaining combinations of “chr/M/MT” to the AN tag.

- **-H, --no-header**

  Do not print the @HD header line.

- **-l, --alt** *FILE*

  Add an AH tag to each sequence listed in the specified [*bwa*(1)](/bwa/1.md)-style **.alt** file. These files use SAM records to represent alternate locus sequences (as named in the **QNAME** field) and their mappings to the primary assembly.

- **-o, --output** *FILE*

  Output to *FILE* \[stdout\].

- **-s, --species** *STR*

  Specify the species for the SP tag.

- **-u, --uri** *STR*

  Specify the URI for the UR tag. Defaults to the absolute path of *ref.fasta* unless reading from stdin.

## AUTHOR

Written by Shane McCarthy from the Sanger Institute.

## SEE ALSO

[*samtools*(1)](/samtools/1.md), [*bcftools*(1)](/bcftools/1.md), [*bwa*(1)](/bwa/1.md), [*sam*(5)](/sam/5.md), [*tabix*(1)](/tabix/1.md)

Samtools website: \<http://www.htslib.org/\>\
 File format specification of SAM/BAM,CRAM,VCF/BCF: \<http://samtools.github.io/hts-specs\>\
 Samtools latest source: \<https://github.com/samtools/samtools\>\
 HTSlib latest source: \<https://github.com/samtools/htslib\>\
 Bcftools website: \<http://samtools.github.io/bcftools\>