Manual page from samtools-1.19
released on 12 December 2023


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


samtools dict ref.fasta|ref.fasta.gz


Create a sequence dictionary file from a fasta file.


-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)-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.


Written by Shane McCarthy from the Sanger Institute.


samtools (1), bcftools (1), bwa(1), sam (5), tabix (1)

Samtools website: <>
File format specification of SAM/BAM,CRAM,VCF/BCF: <>
Samtools latest source: <>
HTSlib latest source: <>
Bcftools website: <>