Creates a sequence dictionary for a reference sequence. This tool creates a sequence dictionary file (with ".dict" extension) from a reference sequence provided in FASTA format, which is required by many processing and analysis tools. The output file contains a header but no SAMRecords, and the header contains only sequence records.

The reference sequence can be gzipped (both .fasta and .fasta.gz are supported).

Usage example:

java -jar picard.jar CreateSequenceDictionary \ 
      R=reference.fasta \ 
      O=reference.dict

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Category Reference

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Overview

Create a SAM/BAM file from a fasta containing reference sequence. The output SAM file contains a header but no SAMRecords, and the header contains only sequence records.

CreateSequenceDictionary (Picard) specific arguments

This table summarizes the command-line arguments that are specific to this tool. For more details on each argument, see the list further down below the table or click on an argument name to jump directly to that entry in the list.

Argument name(s)	Default value	Summary
Required Arguments
--REFERENCE  -R		Input reference fasta or fasta.gz
Optional Tool Arguments
--ALT_NAMES  -AN		Optional file containing the alternative names for the contigs. Tools may use this information to consider different contig notations as identical (e.g: 'chr1' and '1'). The alternative names will be put into the appropriate @AN annotation for each contig. No header. First column is the original name, the second column is an alternative name. One contig may have more than one alternative name.
--arguments_file		read one or more arguments files and add them to the command line
--GENOME_ASSEMBLY  -AS		Put into AS field of sequence dictionary entry if supplied
--help  -h	false	display the help message
--NUM_SEQUENCES	2147483647	Stop after writing this many sequences. For testing.
--OUTPUT  -O		Output SAM file containing only the sequence dictionary. By default it will use the base name of the input reference with the .dict extension
--SPECIES  -SP		Put into SP field of sequence dictionary entry
--TRUNCATE_NAMES_AT_WHITESPACE	true	Make sequence name the first word from the > line in the fasta file. By default the entire contents of the > line is used, excluding leading and trailing whitespace.
--URI  -UR		Put into UR field of sequence dictionary entry. If not supplied, input reference file is used
--version	false	display the version number for this tool
Optional Common Arguments
--COMPRESSION_LEVEL	5	Compression level for all compressed files created (e.g. BAM and VCF).
--CREATE_INDEX	false	Whether to create an index when writing VCF or coordinate sorted BAM output.
--CREATE_MD5_FILE	false	Whether to create an MD5 digest for any BAM or FASTQ files created.
--MAX_RECORDS_IN_RAM	500000	When writing files that need to be sorted, this will specify the number of records stored in RAM before spilling to disk. Increasing this number reduces the number of file handles needed to sort the file, and increases the amount of RAM needed.
--QUIET	false	Whether to suppress job-summary info on System.err.
--TMP_DIR		One or more directories with space available to be used by this program for temporary storage of working files
--USE_JDK_DEFLATER  -use_jdk_deflater	false	Use the JDK Deflater instead of the Intel Deflater for writing compressed output
--USE_JDK_INFLATER  -use_jdk_inflater	false	Use the JDK Inflater instead of the Intel Inflater for reading compressed input
--VALIDATION_STRINGENCY	STRICT	Validation stringency for all SAM files read by this program. Setting stringency to SILENT can improve performance when processing a BAM file in which variable-length data (read, qualities, tags) do not otherwise need to be decoded.
--VERBOSITY	INFO	Control verbosity of logging.
Advanced Arguments
--showHidden	false	display hidden arguments

Argument details

Arguments in this list are specific to this tool. Keep in mind that other arguments are available that are shared with other tools (e.g. command-line GATK arguments); see Inherited arguments above.

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--ALT_NAMES / -AN

Optional file containing the alternative names for the contigs. Tools may use this information to consider different contig notations as identical (e.g: 'chr1' and '1'). The alternative names will be put into the appropriate @AN annotation for each contig. No header. First column is the original name, the second column is an alternative name. One contig may have more than one alternative name.

File  null

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--arguments_file

read one or more arguments files and add them to the command line

List[File]  []

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--COMPRESSION_LEVEL

Compression level for all compressed files created (e.g. BAM and VCF).

int  5  [ [ -∞  ∞ ] ]

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--CREATE_INDEX

Whether to create an index when writing VCF or coordinate sorted BAM output.

Boolean  false

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--CREATE_MD5_FILE

Whether to create an MD5 digest for any BAM or FASTQ files created.

boolean  false

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--GENOME_ASSEMBLY / -AS

Put into AS field of sequence dictionary entry if supplied

String  null

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--help / -h

display the help message

boolean  false

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--MAX_RECORDS_IN_RAM

When writing files that need to be sorted, this will specify the number of records stored in RAM before spilling to disk. Increasing this number reduces the number of file handles needed to sort the file, and increases the amount of RAM needed.

Integer  500000  [ [ -∞  ∞ ] ]

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--NUM_SEQUENCES

Stop after writing this many sequences. For testing.

int  2147483647  [ [ -∞  ∞ ] ]

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--OUTPUT / -O

Output SAM file containing only the sequence dictionary. By default it will use the base name of the input reference with the .dict extension

PicardHtsPath  null

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--QUIET

Whether to suppress job-summary info on System.err.

Boolean  false

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--REFERENCE / -R

Input reference fasta or fasta.gz

R PicardHtsPath  null

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--showHidden / -showHidden

display hidden arguments

boolean  false

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--SPECIES / -SP

Put into SP field of sequence dictionary entry

String  null

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--TMP_DIR

One or more directories with space available to be used by this program for temporary storage of working files

List[File]  []

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--TRUNCATE_NAMES_AT_WHITESPACE

Make sequence name the first word from the > line in the fasta file. By default the entire contents of the > line is used, excluding leading and trailing whitespace.

boolean  true

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--URI / -UR

Put into UR field of sequence dictionary entry. If not supplied, input reference file is used

String  null

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--USE_JDK_DEFLATER / -use_jdk_deflater

Use the JDK Deflater instead of the Intel Deflater for writing compressed output

Boolean  false

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--USE_JDK_INFLATER / -use_jdk_inflater

Use the JDK Inflater instead of the Intel Inflater for reading compressed input

Boolean  false

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--VALIDATION_STRINGENCY

Validation stringency for all SAM files read by this program. Setting stringency to SILENT can improve performance when processing a BAM file in which variable-length data (read, qualities, tags) do not otherwise need to be decoded.

The --VALIDATION_STRINGENCY argument is an enumerated type (ValidationStringency), which can have one of the following values:

STRICT

LENIENT

SILENT

ValidationStringency  STRICT

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--VERBOSITY

Control verbosity of logging.

The --VERBOSITY argument is an enumerated type (LogLevel), which can have one of the following values:

ERROR

WARNING

INFO

DEBUG

LogLevel  INFO

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--version

display the version number for this tool

boolean  false

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GATK version 4.6.0.0 built at Sat, 29 Jun 2024 20:47:29 -0400.