1samtools-dict(1)             Bioinformatics tools             samtools-dict(1)
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NAME

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

9       samtools dict ref.fasta|ref.fasta.gz
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DESCRIPTION

13       Create a sequence dictionary file from a fasta file.
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OPTIONS

17       -a, --assembly STR
18                  Specify the assembly for the AS tag.
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20       -A, --alias, --alternative-name
21                  Add an AN tag with the same value as the SN tag, except that
22                  a “chr” prefix is removed if SN has one or added if it  does
23                  not.   For  mitochondria (i.e., when SN is “M” or “MT”, with
24                  or without a “chr” prefix), also adds the remaining combina‐
25                  tions of “chr/M/MT” to the AN tag.
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27       -H, --no-header
28                  Do not print the @HD header line.
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30       -o, --output FILE
31                  Output to FILE [stdout].
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33       -s, --species STR
34                  Specify the species for the SP tag.
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36       -u, --uri STR
37                  Specify  the  URI  for  the UR tag. Defaults to the absolute
38                  path of ref.fasta unless reading from stdin.
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AUTHOR

42       Written by Shane McCarthy from the Sanger Institute.
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SEE ALSO

46       samtools(1), bcftools(1), sam(5), tabix(1)
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48       Samtools website: <http://www.htslib.org/>
49       File  format  specification   of   SAM/BAM,CRAM,VCF/BCF:   <http://sam‐
50       tools.github.io/hts-specs>
51       Samtools latest source: <https://github.com/samtools/samtools>
52       HTSlib latest source: <https://github.com/samtools/htslib>
53       Bcftools website: <http://samtools.github.io/bcftools>
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57samtools-1.15.1                  7 April 2022                 samtools-dict(1)