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>