NAME

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

SYNOPSIS

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.
-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.