Package picard.sam

Class AddOrReplaceReadGroups

java.lang.Object

picard.cmdline.CommandLineProgram

picard.sam.AddOrReplaceReadGroups

@DocumentedFeature
public class AddOrReplaceReadGroups
extends CommandLineProgram

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

"^[ -~]+$"

(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.

Field Summary

Fields

Modifier and Type	Field	Description
String	INPUT
File	OUTPUT
static final String	READGROUP_ID_REGEX
String	RGCN
String	RGDS
htsjdk.samtools.util.Iso8601Date	RGDT
String	RGFO
String	RGID
String	RGKS
String	RGLB
String	RGPG
Integer	RGPI
String	RGPL
String	RGPM
String	RGPU
String	RGSM
htsjdk.samtools.SAMFileHeader.SortOrder	SORT_ORDER

Fields inherited from class picard.cmdline.CommandLineProgram

COMPRESSION_LEVEL, CREATE_INDEX, CREATE_MD5_FILE, MAX_ALLOWABLE_ONE_LINE_SUMMARY_LENGTH, MAX_RECORDS_IN_RAM, QUIET, REFERENCE_SEQUENCE, referenceSequence, specialArgumentsCollection, SYNTAX_TRANSITION_URL, TMP_DIR, USE_JDK_DEFLATER, USE_JDK_INFLATER, VALIDATION_STRINGENCY, VERBOSITY

Constructor Summary

Constructors

Constructor	Description
AddOrReplaceReadGroups()

Method Summary

Modifier and Type	Method	Description
protected String[]	customCommandLineValidation()	Put any custom command-line validation in an override of this method.
protected int	doWork()	Do the work after command line has been parsed.

Methods inherited from class picard.cmdline.CommandLineProgram

checkRInstallation, getCommandLine, getCommandLineParser, getCommandLineParserForArgs, getDefaultHeaders, getFaqLink, getMetricsFile, getPGRecord, getStandardUsagePreamble, getStandardUsagePreamble, getVersion, hasWebDocumentation, instanceMain, instanceMainWithExit, makeReferenceArgumentCollection, parseArgs, requiresReference, setDefaultHeaders, useLegacyParser

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Details

READGROUP_ID_REGEX

public static final String READGROUP_ID_REGEX

See Also:

• Constant Field Values

INPUT

@Argument(shortName="I",
          doc="Input file (BAM or SAM or a GA4GH url).")
public String INPUT

OUTPUT

@Argument(shortName="O",
          doc="Output file (SAM, BAM or CRAM).")
public File OUTPUT

SORT_ORDER

@Argument(shortName="SO",
          optional=true,
          doc="Optional sort order to output in. If not supplied OUTPUT is in the same order as INPUT.")
public htsjdk.samtools.SAMFileHeader.SortOrder SORT_ORDER

RGID

@Argument(shortName="ID",
          doc="Read-Group ID")
public String RGID

RGLB

@Argument(shortName="LB",
          doc="Read-Group library")
public String RGLB

RGPL

@Argument(shortName="PL",
          doc="Read-Group platform (e.g. ILLUMINA, SOLID)")
public String RGPL

RGPU

@Argument(shortName="PU",
          doc="Read-Group platform unit (eg. run barcode)")
public String RGPU

RGSM

@Argument(shortName="SM",
          doc="Read-Group sample name")
public String RGSM

RGCN

@Argument(shortName="CN",
          doc="Read-Group sequencing center name",
          optional=true)
public String RGCN

RGDS

@Argument(shortName="DS",
          doc="Read-Group description",
          optional=true)
public String RGDS

RGDT

@Argument(shortName="DT",
          doc="Read-Group run date",
          optional=true)
public htsjdk.samtools.util.Iso8601Date RGDT

RGKS

@Argument(shortName="KS",
          doc="Read-Group key sequence",
          optional=true)
public String RGKS

RGFO

@Argument(shortName="FO",
          doc="Read-Group flow order",
          optional=true)
public String RGFO

RGPI

@Argument(shortName="PI",
          doc="Read-Group predicted insert size",
          optional=true)
public Integer RGPI

RGPG

@Argument(shortName="PG",
          doc="Read-Group program group",
          optional=true)
public String RGPG

RGPM

@Argument(shortName="PM",
          doc="Read-Group platform model",
          optional=true)
public String RGPM

Constructor Details

AddOrReplaceReadGroups

public AddOrReplaceReadGroups()

Method Details

doWork

protected int doWork()

Description copied from class: CommandLineProgram

Do the work after command line has been parsed. RuntimeException may be thrown by this method, and are reported appropriately.

Specified by:

doWork in class CommandLineProgram

Returns:

program exit status.

customCommandLineValidation

protected String[] customCommandLineValidation()

Description copied from class: CommandLineProgram

Put any custom command-line validation in an override of this method. clp is initialized at this point and can be used to print usage and access argv. Any options set by command-line parser can be validated.

Overrides:

customCommandLineValidation in class CommandLineProgram

Returns:

null if command line is valid. If command line is invalid, returns an array of error message to be written to the appropriate place.