1samtools-dict(1)             Bioinformatics tools             samtools-dict(1)
2
3
4

NAME

6       samtools dict - create a sequence dictionary file from a fasta file
7

SYNOPSIS

9       samtools dict ref.fasta|ref.fasta.gz
10
11

DESCRIPTION

13       Create a sequence dictionary file from a fasta file.
14
15

OPTIONS

17       -a, --assembly STR
18                  Specify the assembly for the AS tag.
19
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.
26
27       -H, --no-header
28                  Do not print the @HD header line.
29
30       -o, --output FILE
31                  Output to FILE [stdout].
32
33       -s, --species STR
34                  Specify the species for the SP tag.
35
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.
39
40

AUTHOR

42       Written by Shane McCarthy from the Sanger Institute.
43
44

SEE ALSO

46       samtools(1), bcftools(1), sam(5), tabix(1)
47
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>
54
55
56
57samtools-1.13                     7 July 2021                 samtools-dict(1)