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
Category Reference
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. | |
--GA4GH_CLIENT_SECRETS |
client_secrets.json | Google Genomics API client_secrets.json file path. | |
--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.
--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
--arguments_file
read one or more arguments files and add them to the command line
List[File] []
--COMPRESSION_LEVEL
Compression level for all compressed files created (e.g. BAM and VCF).
int 5 [ [ -∞ ∞ ] ]
--CREATE_INDEX
Whether to create an index when writing VCF or coordinate sorted BAM output.
Boolean false
--CREATE_MD5_FILE
Whether to create an MD5 digest for any BAM or FASTQ files created.
boolean false
--GA4GH_CLIENT_SECRETS
Google Genomics API client_secrets.json file path.
String client_secrets.json
--GENOME_ASSEMBLY / -AS
Put into AS field of sequence dictionary entry if supplied
String null
--help / -h
display the help message
boolean false
--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 [ [ -∞ ∞ ] ]
--NUM_SEQUENCES
Stop after writing this many sequences. For testing.
int 2147483647 [ [ -∞ ∞ ] ]
--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
File null
--QUIET
Whether to suppress job-summary info on System.err.
Boolean false
--REFERENCE / -R
Input reference fasta or fasta.gz
R File null
--showHidden / -showHidden
display hidden arguments
boolean false
--SPECIES / -SP
Put into SP field of sequence dictionary entry
String null
--TMP_DIR
One or more directories with space available to be used by this program for temporary storage of working files
List[File] []
--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
--URI / -UR
Put into UR field of sequence dictionary entry. If not supplied, input reference file is used
String null
--USE_JDK_DEFLATER / -use_jdk_deflater
Use the JDK Deflater instead of the Intel Deflater for writing compressed output
Boolean false
--USE_JDK_INFLATER / -use_jdk_inflater
Use the JDK Inflater instead of the Intel Inflater for reading compressed input
Boolean false
--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
--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
--version
display the version number for this tool
boolean false
GATK version 4.2.4.0-SNAPSHOT built at Thu, 16 Dec 2021 11:57:48 -0800.
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