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

       Written by Shane McCarthy from the Sanger Institute.

       Create a sequence dictionary file from a fasta file.

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

-a,--assemblySTR
                  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,--altFILE
                  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,--outputFILE
                  Output to FILE [stdout].

       -s,--speciesSTR
                  Specify the species for the SP tag.

       -u,--uriSTR
                  Specify the URI for the UR tag. Defaults to the absolute path of ref.fasta unless reading from
                  stdin.

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)

       samtools dict ref.fasta|ref.fasta.gz