samtools-dict1

Usage

Overview

Create a sequence dictionary file from a fasta file.

Options

-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.