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samtools-dict(1) Bioinformatics tools samtools-dict(1) 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 repre- sent 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://sam- tools.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-1.23.1 18 March 2026 samtools-dict(1)
NAME | SYNOPSIS | DESCRIPTION | OPTIONS | AUTHOR | SEE ALSO
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