picard.sam.markduplicates

Class MarkDuplicates

java.lang.Object

picard.cmdline.CommandLineProgram

picard.sam.markduplicates.util.AbstractOpticalDuplicateFinderCommandLineProgram

picard.sam.markduplicates.util.AbstractMarkDuplicatesCommandLineProgram

picard.sam.markduplicates.MarkDuplicates

Direct Known Subclasses:

SimpleMarkDuplicatesWithMateCigar

@DocumentedFeature
public class MarkDuplicates
extends AbstractMarkDuplicatesCommandLineProgram

A better duplication marking algorithm that handles all cases including clipped and gapped alignments.

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
static class	MarkDuplicates.DuplicateTaggingPolicy Enum used to control how duplicates are flagged in the DT optional tag on each read.
static class	MarkDuplicates.DuplicateType Enum for the possible values that a duplicate read can be tagged with in the DT attribute.

Nested classes/interfaces inherited from class picard.sam.markduplicates.util.AbstractMarkDuplicatesCommandLineProgram

AbstractMarkDuplicatesCommandLineProgram.SamHeaderAndIterator

Field Summary

Fields

Modifier and Type	Field and Description
java.lang.String	BARCODE_TAG
boolean	CLEAR_DT
boolean	DUPLEX_UMI
static java.lang.String	DUPLICATE_SET_INDEX_TAG The attribute in the SAM/BAM file used to store which read was selected as representative out of a duplicate set
static java.lang.String	DUPLICATE_SET_SIZE_TAG The attribute in the SAM/BAM file used to store the size of a duplicate set
static java.lang.String	DUPLICATE_TYPE_LIBRARY The duplicate type tag value for duplicate type: library.
static java.lang.String	DUPLICATE_TYPE_SEQUENCING The duplicate type tag value for duplicate type: sequencing (optical & pad-hopping, or "co-localized").
static java.lang.String	DUPLICATE_TYPE_TAG The optional attribute in SAM/BAM files used to store the duplicate type.
protected LibraryIdGenerator	libraryIdGenerator
int	MAX_FILE_HANDLES_FOR_READ_ENDS_MAP
int	MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP If more than this many sequences in SAM file, don't spill to disk because there will not be enough file handles.
java.lang.String	MOLECULAR_IDENTIFIER_TAG
java.lang.String	READ_ONE_BARCODE_TAG
java.lang.String	READ_TWO_BARCODE_TAG
boolean	REMOVE_SEQUENCING_DUPLICATES
double	SORTING_COLLECTION_SIZE_RATIO
boolean	TAG_DUPLICATE_SET_MEMBERS
MarkDuplicates.DuplicateTaggingPolicy	TAGGING_POLICY

Fields inherited from class picard.sam.markduplicates.util.AbstractMarkDuplicatesCommandLineProgram

ASSUME_SORT_ORDER, ASSUME_SORTED, COMMENT, DUPLICATE_SCORING_STRATEGY, INPUT, METRICS_FILE, OUTPUT, pgIdsSeen, pgTagArgumentCollection, PROGRAM_GROUP_COMMAND_LINE, PROGRAM_GROUP_NAME, PROGRAM_GROUP_VERSION, PROGRAM_RECORD_ID, REMOVE_DUPLICATES

Fields inherited from class picard.sam.markduplicates.util.AbstractOpticalDuplicateFinderCommandLineProgram

LOG, MAX_OPTICAL_DUPLICATE_SET_SIZE, OPTICAL_DUPLICATE_PIXEL_DISTANCE, opticalDuplicateFinder, READ_NAME_REGEX

Fields inherited from class picard.cmdline.CommandLineProgram

COMPRESSION_LEVEL, CREATE_INDEX, CREATE_MD5_FILE, GA4GH_CLIENT_SECRETS, MAX_ALLOWABLE_ONE_LINE_SUMMARY_LENGTH, MAX_RECORDS_IN_RAM, QUIET, REFERENCE_SEQUENCE, referenceSequence, specialArgumentsCollection, TMP_DIR, USE_JDK_DEFLATER, USE_JDK_INFLATER, VALIDATION_STRINGENCY, VERBOSITY

Constructor Summary

Constructors

Constructor and Description
MarkDuplicates()

Method Summary

Modifier and Type	Method and Description
protected int	doWork() Main work method.

Methods inherited from class picard.sam.markduplicates.util.AbstractMarkDuplicatesCommandLineProgram

addDuplicateReadToMetrics, addReadToLibraryMetrics, addSingletonToCount, finalizeAndWriteMetrics, getChainedPgIds, openInputs, trackOpticalDuplicates

Methods inherited from class picard.sam.markduplicates.util.AbstractOpticalDuplicateFinderCommandLineProgram

customCommandLineValidation, setupOpticalDuplicateFinder

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 Detail

DUPLICATE_TYPE_TAG

public static final java.lang.String DUPLICATE_TYPE_TAG

The optional attribute in SAM/BAM files used to store the duplicate type.

See Also:

Constant Field Values

DUPLICATE_TYPE_LIBRARY

public static final java.lang.String DUPLICATE_TYPE_LIBRARY

The duplicate type tag value for duplicate type: library.

See Also:

Constant Field Values

DUPLICATE_TYPE_SEQUENCING

public static final java.lang.String DUPLICATE_TYPE_SEQUENCING

The duplicate type tag value for duplicate type: sequencing (optical & pad-hopping, or "co-localized").

See Also:

Constant Field Values

DUPLICATE_SET_INDEX_TAG

public static final java.lang.String DUPLICATE_SET_INDEX_TAG

The attribute in the SAM/BAM file used to store which read was selected as representative out of a duplicate set

See Also:

Constant Field Values

DUPLICATE_SET_SIZE_TAG

public static final java.lang.String DUPLICATE_SET_SIZE_TAG

The attribute in the SAM/BAM file used to store the size of a duplicate set

See Also:

Constant Field Values

MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP

@Argument(shortName="MAX_SEQS",
          doc="This option is obsolete. ReadEnds will always be spilled to disk.")
public int MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP

If more than this many sequences in SAM file, don't spill to disk because there will not be enough file handles.

MAX_FILE_HANDLES_FOR_READ_ENDS_MAP

@Argument(shortName="MAX_FILE_HANDLES",
          doc="Maximum number of file handles to keep open when spilling read ends to disk. Set this number a little lower than the per-process maximum number of file that may be open. This number can be found by executing the \'ulimit -n\' command on a Unix system.")
public int MAX_FILE_HANDLES_FOR_READ_ENDS_MAP

SORTING_COLLECTION_SIZE_RATIO

@Argument(doc="This number, plus the maximum RAM available to the JVM, determine the memory footprint used by some of the sorting collections.  If you are running out of memory, try reducing this number.")
public double SORTING_COLLECTION_SIZE_RATIO

BARCODE_TAG

@Argument(doc="Barcode SAM tag (ex. BC for 10X Genomics)",
          optional=true)
public java.lang.String BARCODE_TAG

READ_ONE_BARCODE_TAG

@Argument(doc="Read one barcode SAM tag (ex. BX for 10X Genomics)",
          optional=true)
public java.lang.String READ_ONE_BARCODE_TAG

READ_TWO_BARCODE_TAG

@Argument(doc="Read two barcode SAM tag (ex. BX for 10X Genomics)",
          optional=true)
public java.lang.String READ_TWO_BARCODE_TAG

TAG_DUPLICATE_SET_MEMBERS

@Argument(doc="If a read appears in a duplicate set, add two tags. The first tag, DUPLICATE_SET_SIZE_TAG (DS), indicates the size of the duplicate set. The smallest possible DS value is 2 which occurs when two reads map to the same portion of the reference only one of which is marked as duplicate. The second tag, DUPLICATE_SET_INDEX_TAG (DI), represents a unique identifier for the duplicate set to which the record belongs. This identifier is the index-in-file of the representative read that was selected out of the duplicate set.",
          optional=true)
public boolean TAG_DUPLICATE_SET_MEMBERS

REMOVE_SEQUENCING_DUPLICATES

@Argument(doc="If true remove \'optical\' duplicates and other duplicates that appear to have arisen from the sequencing process instead of the library preparation process, even if REMOVE_DUPLICATES is false. If REMOVE_DUPLICATES is true, all duplicates are removed and this option is ignored.")
public boolean REMOVE_SEQUENCING_DUPLICATES

TAGGING_POLICY

@Argument(doc="Determines how duplicate types are recorded in the DT optional attribute.")
public MarkDuplicates.DuplicateTaggingPolicy TAGGING_POLICY

CLEAR_DT

@Argument(doc="Clear DT tag from input SAM records. Should be set to false if input SAM doesn\'t have this tag.  Default true")
public boolean CLEAR_DT

DUPLEX_UMI

@Argument(doc="Treat UMIs as being duplex stranded.  This option requires that the UMI consist of two equal length strings that are separated by a hyphen (e.g. \'ATC-GTC\'). Reads are considered duplicates if, in addition to standard definition, have identical normalized UMIs.  A UMI from the \'bottom\' strand is normalized by swapping its content around the hyphen (eg. ATC-GTC becomes GTC-ATC).  A UMI from the \'top\' strand is already normalized as it is. Both reads from a read pair considered top strand if the read 1 unclipped 5\' coordinate is less than the read 2 unclipped 5\' coordinate. All chimeric reads and read fragments are treated as having come from the top strand. With this option is it required that the BARCODE_TAG hold non-normalized UMIs. Default false.")
public boolean DUPLEX_UMI

MOLECULAR_IDENTIFIER_TAG

@Argument(doc="SAM tag to uniquely identify the molecule from which a read was derived.  Use of this option requires that the BARCODE_TAG option be set to a non null value.  Default null.",
          optional=true)
public java.lang.String MOLECULAR_IDENTIFIER_TAG

libraryIdGenerator

protected LibraryIdGenerator libraryIdGenerator

Constructor Detail

MarkDuplicates

public MarkDuplicates()

Method Detail

doWork

protected int doWork()

Main work method. Reads the BAM file once and collects sorted information about the 5' ends of both ends of each read (or just one end in the case of pairs). Then makes a pass through those determining duplicates before re-reading the input file and writing it out with duplication flags set correctly.

Specified by:

doWork in class CommandLineProgram

Returns:

program exit status.