Not to be confused with SortSam which sorts a SAM or BAM file with a valid sequence dictionary, ReorderSam reorders reads in a SAM/BAM file to match the contig ordering in a provided reference file, as determined by exact name matching of contigs. Reads mapped to contigs absent in the new reference are unmapped. Runs substantially faster if the input is an indexed BAM file. Example java -jar picard.jar ReorderSam \ INPUT=sample.bam \ OUTPUT=reordered.bam \ SEQUENCE_DICTIONARY=reference_with_different_order.dict
Category Read Data Manipulation
Overview
Reorders a SAM/BAM input file according to the order of contigs in a second reference file.Summary
Not to be confused with SortSam which sorts a SAM or BAM file with a valid sequence dictionary, ReorderSam reorders reads in a SAM/BAM file to match the contig ordering in a provided reference file, as determined by exact name matching of contigs. Reads mapped to contigs absent in the new reference are unmapped. Runs substantially faster if the input is an indexed BAM file.Example
java -jar picard.jar ReorderSam \ INPUT=sample.bam \ OUTPUT=reordered.bam \ SEQUENCE_DICTIONARY=reference_with_different_order.dict
Caveats
Note that REFERENCE_SEQUENCE is used for reading the INPUT, (e.g. when reading cram files) not for determining the order of the OUTPUT. For that you must specify the SEQUENCE_DICTIONARY argument.ReorderSam (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 | |||
--INPUT -I |
Input file (SAM or BAM) to extract reads from. | ||
--OUTPUT -O |
Output file (SAM or BAM) to write extracted reads to. | ||
--SEQUENCE_DICTIONARY -SD |
A Sequence Dictionary for the OUTPUT file (can be read from one of the following file types (SAM, BAM, VCF, BCF, Interval List, Fasta, or Dict) | ||
Optional Tool Arguments | |||
--ALLOW_CONTIG_LENGTH_DISCORDANCE -U |
false | If true, then permits mapping from a read contig to a new reference contig with the same name but a different length. Highly dangerous, only use if you know what you are doing. | |
--ALLOW_INCOMPLETE_DICT_CONCORDANCE -S |
false | If true, allows only a partial overlap of the original contigs with the new reference sequence contigs. By default, this tool requires a corresponding contig in the new reference for each read contig | |
--arguments_file |
read one or more arguments files and add them to the command line | ||
--help -h |
false | display the help message | |
--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. | |
--REFERENCE_SEQUENCE -R |
Reference sequence file. | ||
--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.
--ALLOW_CONTIG_LENGTH_DISCORDANCE / -U
If true, then permits mapping from a read contig to a new reference contig with the same name but a different length. Highly dangerous, only use if you know what you are doing.
boolean false
--ALLOW_INCOMPLETE_DICT_CONCORDANCE / -S
If true, allows only a partial overlap of the original contigs with the new reference sequence contigs. By default, this tool requires a corresponding contig in the new reference for each read contig
boolean false
--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
--help / -h
display the help message
boolean false
--INPUT / -I
Input file (SAM or BAM) to extract reads from.
R File null
--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 [ [ -∞ ∞ ] ]
--OUTPUT / -O
Output file (SAM or BAM) to write extracted reads to.
R File null
--QUIET
Whether to suppress job-summary info on System.err.
Boolean false
--REFERENCE_SEQUENCE / -R
Reference sequence file.
File null
--SEQUENCE_DICTIONARY / -SD
A Sequence Dictionary for the OUTPUT file (can be read from one of the following file types (SAM, BAM, VCF, BCF, Interval List, Fasta, or Dict)
R File null
--showHidden / -showHidden
display hidden arguments
boolean false
--TMP_DIR
One or more directories with space available to be used by this program for temporary storage of working files
List[File] []
--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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