Examines aligned records in the supplied SAM or BAM file to locate duplicate molecules. All records are then written to the output file with the duplicate records flagged.

Category Read Data Manipulation

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Overview

This is a simple tool to mark duplicates using the DuplicateSetIterator, DuplicateSet, and SAMRecordDuplicateComparator. Users should continue to use MarkDuplicates in general. The main motivation of this tool was the fact that MarkDuplicates has many, many, many useful test cases, but few unit tests for validating individual duplicate sets. To test the DuplicateSetIterator, DuplicateSet, and SAMRecordDuplicateComparator, the most expedient method was to write this tool and make sure it behaves similarly to MarkDuplicates. Not the best, I know, but good enough. NH 06/25/2015. See MarkDuplicates for more details.

SimpleMarkDuplicatesWithMateCigar (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	[]	One or more input SAM or BAM files to analyze. Must be coordinate sorted.
--METRICS_FILE  -M	null	File to write duplication metrics to
--OUTPUT  -O	null	The output file to write marked records to
Optional Tool Arguments
--arguments_file	[]	read one or more arguments files and add them to the command line
--ASSUME_SORT_ORDER  -ASO	null	If not null, assume that the input file has this order even if the header says otherwise.
--BARCODE_TAG	null	Barcode SAM tag (ex. BC for 10X Genomics)
--CLEAR_DT	true	Clear DT tag from input SAM records. Should be set to false if input SAM doesn't have this tag. Default true
--COMMENT  -CO	[]	Comment(s) to include in the output file's header.
--DUPLICATE_SCORING_STRATEGY  -DS	SUM_OF_BASE_QUALITIES	The scoring strategy for choosing the non-duplicate among candidates.
--help  -h	false	display the help message
--MAX_FILE_HANDLES_FOR_READ_ENDS_MAP  -MAX_FILE_HANDLES	8000	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.
--MAX_OPTICAL_DUPLICATE_SET_SIZE	300000	This number is the maximum size of a set of duplicate reads for which we will attempt to determine which are optical duplicates. Please be aware that if you raise this value too high and do encounter a very large set of duplicate reads, it will severely affect the runtime of this tool. To completely disable this check, set the value to -1.
--MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP  -MAX_SEQS	50000	This option is obsolete. ReadEnds will always be spilled to disk.
--OPTICAL_DUPLICATE_PIXEL_DISTANCE	100	The maximum offset between two duplicate clusters in order to consider them optical duplicates. The default is appropriate for unpatterned versions of the Illumina platform. For the patterned flowcell models, 2500 is moreappropriate. For other platforms and models, users should experiment to find what works best.
--PROGRAM_GROUP_COMMAND_LINE  -PG_COMMAND	null	Value of CL tag of PG record to be created. If not supplied the command line will be detected automatically.
--PROGRAM_GROUP_NAME  -PG_NAME	SimpleMarkDuplicatesWithMateCigar	Value of PN tag of PG record to be created.
--PROGRAM_GROUP_VERSION  -PG_VERSION	null	Value of VN tag of PG record to be created. If not specified, the version will be detected automatically.
--PROGRAM_RECORD_ID  -PG	MarkDuplicates	The program record ID for the @PG record(s) created by this program. Set to null to disable PG record creation. This string may have a suffix appended to avoid collision with other program record IDs.
--READ_NAME_REGEX		Regular expression that can be used to parse read names in the incoming SAM file. Read names are parsed to extract three variables: tile/region, x coordinate and y coordinate. These values are used to estimate the rate of optical duplication in order to give a more accurate estimated library size. Set this option to null to disable optical duplicate detection, e.g. for RNA-seq or other data where duplicate sets are extremely large and estimating library complexity is not an aim. Note that without optical duplicate counts, library size estimation will be inaccurate. The regular expression should contain three capture groups for the three variables, in order. It must match the entire read name. Note that if the default regex is specified, a regex match is not actually done, but instead the read name is split on colon character. For 5 element names, the 3rd, 4th and 5th elements are assumed to be tile, x and y values. For 7 element names (CASAVA 1.8), the 5th, 6th, and 7th elements are assumed to be tile, x and y values.
--READ_ONE_BARCODE_TAG	null	Read one barcode SAM tag (ex. BX for 10X Genomics)
--READ_TWO_BARCODE_TAG	null	Read two barcode SAM tag (ex. BX for 10X Genomics)
--REMOVE_DUPLICATES	false	If true do not write duplicates to the output file instead of writing them with appropriate flags set.
--REMOVE_SEQUENCING_DUPLICATES	false	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.
--SORTING_COLLECTION_SIZE_RATIO	0.25	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.
--TAG_DUPLICATE_SET_MEMBERS	false	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.
--TAGGING_POLICY	DontTag	Determines how duplicate types are recorded in the DT optional attribute.
--version	false	display the version number for this tool
Optional Common Arguments
--ADD_PG_TAG_TO_READS	true	Add PG tag to each read in a SAM or BAM
--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
Deprecated Arguments
--ASSUME_SORTED  -AS	false	If true, assume that the input file is coordinate sorted even if the header says otherwise. Deprecated, used ASSUME_SORT_ORDER=coordinate instead.

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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--ADD_PG_TAG_TO_READS / NA

Add PG tag to each read in a SAM or BAM

Boolean  true

---

--arguments_file / NA

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

List[File]  []

---

--ASSUME_SORT_ORDER / -ASO

If not null, assume that the input file has this order even if the header says otherwise.

Exclusion: This argument cannot be used at the same time as ASSUME_SORTED.

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

unsorted

queryname

coordinate

duplicate

unknown

SortOrder  null

---

--ASSUME_SORTED / -AS

If true, assume that the input file is coordinate sorted even if the header says otherwise. Deprecated, used ASSUME_SORT_ORDER=coordinate instead.

Exclusion: This argument cannot be used at the same time as ASSUME_SORT_ORDER, ASO.

boolean  false

---

--BARCODE_TAG / NA

Barcode SAM tag (ex. BC for 10X Genomics)

String  null

---

--CLEAR_DT / NA

Clear DT tag from input SAM records. Should be set to false if input SAM doesn't have this tag. Default true

boolean  true

---

--COMMENT / -CO

Comment(s) to include in the output file's header.

List[String]  []

---

--COMPRESSION_LEVEL / NA

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

int  5  [ [ -∞  ∞ ] ]

---

--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

---

--DUPLICATE_SCORING_STRATEGY / -DS

The scoring strategy for choosing the non-duplicate among candidates.

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

SUM_OF_BASE_QUALITIES

TOTAL_MAPPED_REFERENCE_LENGTH

RANDOM

ScoringStrategy  SUM_OF_BASE_QUALITIES

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--GA4GH_CLIENT_SECRETS / NA

Google Genomics API client_secrets.json file path.

String  client_secrets.json

---

--help / -h

display the help message

boolean  false

---

--INPUT / -I

One or more input SAM or BAM files to analyze. Must be coordinate sorted.

R List[String]  []

---

--MAX_FILE_HANDLES_FOR_READ_ENDS_MAP / -MAX_FILE_HANDLES

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.

int  8000  [ [ -∞  ∞ ] ]

---

--MAX_OPTICAL_DUPLICATE_SET_SIZE / NA

This number is the maximum size of a set of duplicate reads for which we will attempt to determine which are optical duplicates. Please be aware that if you raise this value too high and do encounter a very large set of duplicate reads, it will severely affect the runtime of this tool. To completely disable this check, set the value to -1.

long  300000  [ [ -∞  ∞ ] ]

---

--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  [ [ -∞  ∞ ] ]

---

--MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP / -MAX_SEQS

This option is obsolete. ReadEnds will always be spilled to disk.
If more than this many sequences in SAM file, don't spill to disk because there will not be enough file handles.

int  50000  [ [ -∞  ∞ ] ]

---

--METRICS_FILE / -M

File to write duplication metrics to

R File  null

---

--OPTICAL_DUPLICATE_PIXEL_DISTANCE / NA

The maximum offset between two duplicate clusters in order to consider them optical duplicates. The default is appropriate for unpatterned versions of the Illumina platform. For the patterned flowcell models, 2500 is moreappropriate. For other platforms and models, users should experiment to find what works best.

int  100  [ [ -∞  ∞ ] ]

---

--OUTPUT / -O

The output file to write marked records to

R File  null

---

--PROGRAM_GROUP_COMMAND_LINE / -PG_COMMAND

Value of CL tag of PG record to be created. If not supplied the command line will be detected automatically.

String  null

---

--PROGRAM_GROUP_NAME / -PG_NAME

Value of PN tag of PG record to be created.

String  SimpleMarkDuplicatesWithMateCigar

---

--PROGRAM_GROUP_VERSION / -PG_VERSION

Value of VN tag of PG record to be created. If not specified, the version will be detected automatically.

String  null

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--PROGRAM_RECORD_ID / -PG

The program record ID for the @PG record(s) created by this program. Set to null to disable PG record creation. This string may have a suffix appended to avoid collision with other program record IDs.

String  MarkDuplicates

---

--QUIET / NA

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

Boolean  false

---

--READ_NAME_REGEX / NA

Regular expression that can be used to parse read names in the incoming SAM file. Read names are parsed to extract three variables: tile/region, x coordinate and y coordinate. These values are used to estimate the rate of optical duplication in order to give a more accurate estimated library size. Set this option to null to disable optical duplicate detection, e.g. for RNA-seq or other data where duplicate sets are extremely large and estimating library complexity is not an aim. Note that without optical duplicate counts, library size estimation will be inaccurate. The regular expression should contain three capture groups for the three variables, in order. It must match the entire read name. Note that if the default regex is specified, a regex match is not actually done, but instead the read name is split on colon character. For 5 element names, the 3rd, 4th and 5th elements are assumed to be tile, x and y values. For 7 element names (CASAVA 1.8), the 5th, 6th, and 7th elements are assumed to be tile, x and y values.

String  

---

--READ_ONE_BARCODE_TAG / NA

Read one barcode SAM tag (ex. BX for 10X Genomics)

String  null

---

--READ_TWO_BARCODE_TAG / NA

Read two barcode SAM tag (ex. BX for 10X Genomics)

String  null

---

--REFERENCE_SEQUENCE / -R

Reference sequence file.

File  null

---

--REMOVE_DUPLICATES / NA

If true do not write duplicates to the output file instead of writing them with appropriate flags set.

boolean  false

---

--REMOVE_SEQUENCING_DUPLICATES / NA

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.

boolean  false

---

--showHidden / -showHidden

display hidden arguments

boolean  false

---

--SORTING_COLLECTION_SIZE_RATIO / NA

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.

double  0.25  [ [ -∞  ∞ ] ]

---

--TAG_DUPLICATE_SET_MEMBERS / NA

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.

boolean  false

---

--TAGGING_POLICY / NA

Determines how duplicate types are recorded in the DT optional attribute.

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

DontTag

OpticalOnly

All

DuplicateTaggingPolicy  DontTag

---

--TMP_DIR / NA

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 / 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

---

--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

---

--version / NA

display the version number for this tool

boolean  false

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GATK version 4.0.1.2 built at 02-02-2019 02:02:55.