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**EXPERIMENTAL** MarkDuplicatesGATK

Examines aligned records in the supplied SAM/BAM/CRAM file to locate duplicate molecules.

Category Read Data Manipulation


Overview

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

MarkDuplicatesGATK 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/BAM/CRAM 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_SORTED
 -AS
false If true, assume that the input file is coordinate sorted even if the header says otherwise.
--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.
--gcs-max-retries
 -gcs-retries
20 If the GCS bucket channel errors out, how many times it will attempt to re-initiate the connection
--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_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50000 This option is obsolete.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. This should usually be set to some fairly small number (e.g. 5-10 pixels) unless using later versions of the Illumina pipeline that multiply pixel values by 10, in which case 50-100 is more normal.
--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
MarkDuplicatesGATK 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
MarkDuplicatesGATK 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
[a-zA-Z0-9]+:[0-9]:([0-9]+):([0-9]+):([0-9]+).* 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. 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.
--REMOVE_DUPLICATES
false If true do not write duplicates to the output file instead of writing them with appropriate flags set.
--reportMemoryStats
false Report Memory Stats at various times during the run
--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.
--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 GELI).
--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.
--gatk-config-file
null A configuration file to use with the GATK.
--MAX_RECORDS_IN_RAM
500000 When writing SAM 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 a SAM file, and increases the amount of RAM needed.
--QUIET
false Whether to suppress job-summary info on System.err.
--reference
 -R
null Reference sequence file.
--TMP_DIR
[] Undocumented option
--use-jdk-deflater
 -jdk-deflater
false Whether to use the JdkDeflater (as opposed to IntelDeflater)
--use-jdk-inflater
 -jdk-inflater
false Whether to use the JdkInflater (as opposed to IntelInflater)
--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

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.


--arguments_file / NA

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

List[File]  []


--ASSUME_SORTED / -AS

If true, assume that the input file is coordinate sorted even if the header says otherwise.

boolean  false


--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 GELI).

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


--gatk-config-file / NA

A configuration file to use with the GATK.

String  null


--gcs-max-retries / -gcs-retries

If the GCS bucket channel errors out, how many times it will attempt to re-initiate the connection

int  20  [ [ -∞  ∞ ] ]


--help / -h

display the help message

boolean  false


--input / -I

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

R List[File]  []


--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_RECORDS_IN_RAM / NA

When writing SAM 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 a SAM 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. This should usually be set to some fairly small number (e.g. 5-10 pixels) unless using later versions of the Illumina pipeline that multiply pixel values by 10, in which case 50-100 is more normal.

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  MarkDuplicatesGATK


--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


--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  MarkDuplicatesGATK


--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. 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  [a-zA-Z0-9]+:[0-9]:([0-9]+):([0-9]+):([0-9]+).*


--reference / -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


--reportMemoryStats / NA

Report Memory Stats at various times during the run

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  [ [ -∞  ∞ ] ]


--TMP_DIR / NA

Undocumented option

List[File]  []


--use-jdk-deflater / -jdk-deflater

Whether to use the JdkDeflater (as opposed to IntelDeflater)

boolean  false


--use-jdk-inflater / -jdk-inflater

Whether to use the JdkInflater (as opposed to IntelInflater)

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 / -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 / NA

display the version number for this tool

boolean  false


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GATK version 4.0.4.0 built at 23-40-2018 11:40:56.