Showing tool doc from version 4.1.0.0 | The latest version is 4.1.1.0

**EXPERIMENTAL** SimpleMarkDuplicatesWithMateCigar (Picard)

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


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.
--DUPLEX_UMI
false 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.
--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.
--MOLECULAR_IDENTIFIER_TAG
null 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.
--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
MarkDuplicates can use the tile and cluster positions to estimate the rate of optical duplication in addition to the dominant source of duplication, PCR, to provide a more accurate estimation of library size. By default (with no READ_NAME_REGEX specified), MarkDuplicates will attempt to extract coordinates using a split on ':' (see Note below). Set READ_NAME_REGEX to 'null' to disable optical duplicate detection. Note that without optical duplicate counts, library size estimation will be less accurate. If the read name does not follow a standard Illumina colon-separation convention, but does contain tile and x,y coordinates, a regular expression can be specified to extract three variables: tile/region, x coordinate and y coordinate from a read name. The regular expression must contain three capture groups for the three variables, in order. It must match the entire read name. e.g. if field names were separated by semi-colon (';') this example regex could be specified (?:.*;)?([0-9]+)[^;]*;([0-9]+)[^;]*;([0-9]+)[^;]*$ Note that if no READ_NAME_REGEX is specified, the read name is split on ':'. 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.


--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


--DUPLEX_UMI / NA

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.

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


--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


--MOLECULAR_IDENTIFIER_TAG / NA

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.

String  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


--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

MarkDuplicates can use the tile and cluster positions to estimate the rate of optical duplication in addition to the dominant source of duplication, PCR, to provide a more accurate estimation of library size. By default (with no READ_NAME_REGEX specified), MarkDuplicates will attempt to extract coordinates using a split on ':' (see Note below). Set READ_NAME_REGEX to 'null' to disable optical duplicate detection. Note that without optical duplicate counts, library size estimation will be less accurate. If the read name does not follow a standard Illumina colon-separation convention, but does contain tile and x,y coordinates, a regular expression can be specified to extract three variables: tile/region, x coordinate and y coordinate from a read name. The regular expression must contain three capture groups for the three variables, in order. It must match the entire read name. e.g. if field names were separated by semi-colon (';') this example regex could be specified (?:.*;)?([0-9]+)[^;]*;([0-9]+)[^;]*;([0-9]+)[^;]*$ Note that if no READ_NAME_REGEX is specified, the read name is split on ':'. 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


Return to top


See also General Documentation | Tool Docs Index Tool Documentation Index | Support Forum

GATK version 4.1.0.0 built at Wed, 30 Jan 2019 10:21:04 +0530.