samtools-dict - create a sequence dictionary file from a fasta
file
samtools dict ref.fasta|ref.fasta.gz
Create a sequence dictionary file from a fasta file.
- -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.
Written by Shane McCarthy from the Sanger Institute.
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>