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).
'^[ -~]+$' (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.
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.
java -jar picard.jar AddOrReplaceReadGroups \
I=input.bam \
O=output.bam \
RGID=4 \
RGLB=lib1 \
RGPL=illumina \
RGPU=unit1 \
RGSM=20
#READGROUP_ID_REGEX(one or more characters from the ASCII range 32 through 126). In particular
<Space> is the only non-printing character allowed.
RG value will be lost.
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 | |
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.
read one or more arguments files and add them to the command line
List[File] []
Compression level for all compressed files created (e.g. BAM and VCF).
int 5 [ [ -∞ ∞ ] ]
Whether to create a BAM index when writing a coordinate-sorted BAM file.
Boolean false
Whether to create an MD5 digest for any BAM or FASTQ files created.
boolean false
Google Genomics API client_secrets.json file path.
String client_secrets.json
display the help message
boolean false
Input file (BAM or SAM or a GA4GH url).
R String null
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 file (BAM or SAM).
R File null
Whether to suppress job-summary info on System.err.
Boolean false
Reference sequence file.
File null
Read-Group sequencing center name
String null
Read-Group description
String null
Read-Group run date
Iso8601Date null
Read-Group flow order
String null
Read-Group ID
String 1
Read-Group key sequence
String null
Read-Group library
R String null
Read-Group program group
String null
Read-Group predicted insert size
Integer null
Read-Group platform (e.g. illumina, solid)
R String null
Read-Group platform model
String null
Read-Group platform unit (eg. run barcode)
R String null
Read-Group sample name
R String null
display hidden arguments
boolean false
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:
SortOrder null
One or more directories with space available to be used by this program for temporary storage of working files
List[File] []
Use the JDK Deflater instead of the Intel Deflater for writing compressed output
Boolean false
Use the JDK Inflater instead of the Intel Inflater for reading compressed input
Boolean false
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:
ValidationStringency STRICT
Control verbosity of logging.
The --VERBOSITY argument is an enumerated type (LogLevel), which can have one of the following values:
LogLevel INFO
display the version number for this tool
boolean false
See also General Documentation | Tool Docs Index Tool Documentation Index | Support Forum
GATK version 4.0.11.0 built at 23-11-2018 02:11:49.