Assigns all the reads in a file to a single new read-group. This tool accepts INPUT BAM and SAM files or URLs from the Global Alliance for Genomics and Health (GA4GH).

Usage example:

java -jar picard.jar AddOrReplaceReadGroups \ I=input.bam \ O=output.bam \ RGID=4 \ RGLB=lib1 \ RGPL=ILLUMINA \ RGPU=unit1 \ RGSM=20

Caveats

The value of the tags must adhere (according to the SAM-spec) with the regex '^[ -~]+$' (one or more characters from the ASCII range 32 through 126). In particular <Space> is the only non-printing character allowed. The program enables only the wholesale assignment of all the reads in the INPUT to a single read-group. If your file already has reads assigned to multiple read-groups, the original RG value will be lost. For more information about read-groups, see the GATK Dictionary entry.

Category Read Data Manipulation

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Overview

Assigns all the reads in a file to a single new read-group.

Summary

Many tools (Picard and GATK for example) require or assume the presence of at least one RG tag, defining a "read-group" to which each read can be assigned (as specified in the RG tag in the SAM record). This tool enables the user to assign all the reads in the #INPUT to a single new read-group. For more information about read-groups, see the GATK Dictionary entry.
This tool accepts as INPUT BAM and SAM files or URLs from the Global Alliance for Genomics and Health (GA4GH).

Usage example:

 java -jar picard.jar AddOrReplaceReadGroups \
       I=input.bam \
       O=output.bam \
       RGID=4 \
       RGLB=lib1 \
       RGPL=ILLUMINA \
       RGPU=unit1 \
       RGSM=20
 

Caveats

The value of the tags must adhere (according to the SAM-spec) with the regex

#READGROUP_ID_REGEX

(one or more characters from the ASCII range 32 through 126). In particular <Space> is the only non-printing character allowed.
The program enables only the wholesale assignment of all the reads in the #INPUT to a single read-group. If your file already has reads assigned to multiple read-groups, the original RG value will be lost.

AddOrReplaceReadGroups (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 (BAM or SAM or a GA4GH url).
--OUTPUT  -O	null	Output file (BAM or SAM).
--RGLB  -LB	null	Read-Group library
--RGPL  -PL	null	Read-Group platform (e.g. ILLUMINA, SOLID)
--RGPU  -PU	null	Read-Group platform unit (eg. run barcode)
--RGSM  -SM	null	Read-Group sample name
Optional Tool Arguments
--arguments_file	[]	read one or more arguments files and add them to the command line
--help  -h	false	display the help message
--RGCN  -CN	null	Read-Group sequencing center name
--RGDS  -DS	null	Read-Group description
--RGDT  -DT	null	Read-Group run date
--RGFO  -FO	null	Read-Group flow order
--RGID  -ID	1	Read-Group ID
--RGKS  -KS	null	Read-Group key sequence
--RGPG  -PG	null	Read-Group program group
--RGPI  -PI	null	Read-Group predicted insert size
--RGPM  -PM	null	Read-Group platform model
--SORT_ORDER  -SO	null	Optional sort order to output in. If not supplied OUTPUT is in the same order as INPUT.
--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.

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--arguments_file / NA

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

List[File]  []

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--COMPRESSION_LEVEL / NA

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

int  5  [ [ -∞  ∞ ] ]

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--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

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--help / -h

display the help message

boolean  false

---

--INPUT / -I

Input file (BAM or SAM or a GA4GH url).

R String  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 (BAM or SAM).

R File  null

---

--QUIET / NA

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

Boolean  false

---

--REFERENCE_SEQUENCE / -R

Reference sequence file.

File  null

---

--RGCN / -CN

Read-Group sequencing center name

String  null

---

--RGDS / -DS

Read-Group description

String  null

---

--RGDT / -DT

Read-Group run date

Iso8601Date  null

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--RGFO / -FO

Read-Group flow order

String  null

---

--RGID / -ID

Read-Group ID

String  1

---

--RGKS / -KS

Read-Group key sequence

String  null

---

--RGLB / -LB

Read-Group library

R String  null

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--RGPG / -PG

Read-Group program group

String  null

---

--RGPI / -PI

Read-Group predicted insert size

Integer  null

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--RGPL / -PL

Read-Group platform (e.g. ILLUMINA, SOLID)

R String  null

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--RGPM / -PM

Read-Group platform model

String  null

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--RGPU / -PU

Read-Group platform unit (eg. run barcode)

R String  null

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--RGSM / -SM

Read-Group sample name

R String  null

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--showHidden / -showHidden

display hidden arguments

boolean  false

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--SORT_ORDER / -SO

Optional sort order to output in. If not supplied OUTPUT is in the same order as INPUT.

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

unsorted

queryname

coordinate

duplicate

unknown

SortOrder  null

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--TMP_DIR / NA

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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--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 / 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

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--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

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--version / NA

display the version number for this tool

boolean  false

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GATK version 4.1.4.1 built at Thu, 5 Dec 2019 09:51:56 -0500.