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samtools-dict - Man Page

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.


Do not print the @HD header line.

-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.

See Also

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

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>

Referenced By


7 April 2022 samtools-1.15.1 Bioinformatics tools