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)-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), bcftools(1), bwa(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>

samtools-1.21                                   12 September 2024                               samtools-dict(1)