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	null	Input file (SAM or BAM) to extract reads from.
--OUTPUT  -O	null	Output file (SAM or BAM) to write extracted reads to.
--SEQUENCE_DICTIONARY  -SD	null	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 a BAM index when writing a coordinate-sorted BAM file.
--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	null	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 / NA

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

List[File]  []

---

--COMPRESSION_LEVEL / NA

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

int  5  [ [ -∞  ∞ ] ]

---

--CREATE_INDEX / NA

Whether to create a BAM index when writing a coordinate-sorted BAM file.

Boolean  false

---

--CREATE_MD5_FILE / NA

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

boolean  false

---

--GA4GH_CLIENT_SECRETS / NA

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 / NA

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 / NA

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 / NA

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 / NA

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 / NA

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 / NA

display the version number for this tool

boolean  false

---

Return to top

---

GATK version 4.1.6.0-SNAPSHOT built at Thu, 2 Apr 2020 14:54:17 -0400.