1samtools-dict(1) Bioinformatics tools samtools-dict(1)
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6 samtools dict - create a sequence dictionary file from a fasta file
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9 samtools dict ref.fasta|ref.fasta.gz
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13 Create a sequence dictionary file from a fasta file.
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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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42 Written by Shane McCarthy from the Sanger Institute.
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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-1.13 7 July 2021 samtools-dict(1)