AddOrReplaceReadGroups (Picard) – GATK

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

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 {@link #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

{@value #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 {@link #INPUT} to a single read-group. If your file already has reads assigned to multiple read-groups, the original RG value will be lost. @author mdepristo

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		Input file (BAM or SAM or a GA4GH url).
--OUTPUT -O		Output file (SAM, BAM or CRAM).
--RGLB -LB		Read-Group library
--RGPL -PL		Read-Group platform (e.g. ILLUMINA, SOLID)
--RGPU -PU		Read-Group platform unit (eg. run barcode)
--RGSM -SM		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		Read-Group sequencing center name
--RGDS -DS		Read-Group description
--RGDT -DT		Read-Group run date
--RGFO -FO		Read-Group flow order
--RGID -ID	1	Read-Group ID
--RGKS -KS		Read-Group key sequence
--RGPG -PG		Read-Group program group
--RGPI -PI		Read-Group predicted insert size
--RGPM -PM		Read-Group platform model
--SORT_ORDER -SO		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 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.
--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

display hidden arguments

boolean false

--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

--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

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GATK version 4.5.0.0 built at Tue, 9 Jan 2024 14:37:17 -0500.

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Articles in this section

Usage example:

Caveats

Category Read Data Manipulation

Overview

Summary

Usage example:

Caveats

AddOrReplaceReadGroups (Picard) specific arguments

Argument details

--help / -h

--INPUT / -I

--OUTPUT / -O

--REFERENCE_SEQUENCE / -R

--RGCN / -CN

--RGDS / -DS

--RGDT / -DT

--RGFO / -FO

--RGID / -ID

--RGKS / -KS

--RGLB / -LB

--RGPG / -PG

--RGPI / -PI

--RGPL / -PL

--RGPM / -PM

--RGPU / -PU

--RGSM / -SM

--showHidden / -showHidden

--SORT_ORDER / -SO

--USE_JDK_DEFLATER / -use_jdk_deflater

--USE_JDK_INFLATER / -use_jdk_inflater

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