MarkIlluminaAdapters (Picard)

Reads a SAM/BAM/CRAM file and rewrites it with new adapter-trimming tags.

This tool clears any existing adapter-trimming tags (XT:i:) in the optional tag region of the input file. The SAM/BAM/CRAM file must be sorted by query name.

Outputs a metrics file histogram showing counts of bases_clipped per read.

Usage example:

java -jar picard.jar MarkIlluminaAdapters \
 INPUT=input.sam \
METRICS=metrics.txt

Category Base Calling

Overview

Command line program to mark the location of adapter sequences. This also outputs a Histogram of metrics describing the clipped bases @author Tim Fennell (adapted by mborkan@broadinstitute.org)

MarkIlluminaAdapters (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		Undocumented option
--METRICS -M		Histogram showing counts of bases_clipped in how many reads
Optional Tool Arguments
--ADAPTER_TRUNCATION_LENGTH	30	Adapters are truncated to this length to speed adapter matching. Set to a large number to effectively disable truncation.
--ADAPTERS	[INDEXED, DUAL_INDEXED, PAIRED_END]	Which adapters sequences to attempt to identify and clip.
--arguments_file		read one or more arguments files and add them to the command line
--FIVE_PRIME_ADAPTER		For specifying adapters other than standard Illumina
--help -h	false	display the help message
--MAX_ERROR_RATE_PE	0.1	The maximum mismatch error rate to tolerate when clipping paired-end reads.
--MAX_ERROR_RATE_SE	0.1	The maximum mismatch error rate to tolerate when clipping single-end reads.
--MIN_MATCH_BASES_PE	6	The minimum number of bases to match over (per-read) when clipping paired-end reads.
--MIN_MATCH_BASES_SE	12	The minimum number of bases to match over when clipping single-end reads.
--NUM_ADAPTERS_TO_KEEP	1	If pruning the adapter list, keep only this many adapter sequences when pruning the list (plus any adapters that were tied with the adapters being kept).
--OUTPUT -O		If output is not specified, just the metrics are generated
--PAIRED_RUN -PE		DEPRECATED. Whether this is a paired-end run. No longer used.
--PRUNE_ADAPTER_LIST_AFTER_THIS_MANY_ADAPTERS_SEEN -APT	100	If looking for multiple adapter sequences, then after having seen this many adapters, shorten the list of sequences. Keep the adapters that were found most frequently in the input so far. Set to -1 if the input has a heterogeneous mix of adapters so shortening is undesirable.
--THREE_PRIME_ADAPTER		For specifying adapters other than standard Illumina
--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 VCF).
--CREATE_INDEX	false	Whether to create an index when writing VCF or coordinate sorted BAM output.
--CREATE_MD5_FILE	false	Whether to create an MD5 digest for any BAM or FASTQ files created.
--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		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

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.

--ADAPTER_TRUNCATION_LENGTH

Adapters are truncated to this length to speed adapter matching. Set to a large number to effectively disable truncation.

int 30 [ [ -∞ ∞ ] ]

--ADAPTERS

Which adapters sequences to attempt to identify and clip.

The --ADAPTERS argument is an enumerated type (List[IlluminaAdapterPair]), which can have one of the following values:

PAIRED_END: The following sequences can be found in https://support.illumina.com/content/dam/illumina-support/documents/documentation/chemistry_documentation/experiment-design/illumina-adapter-sequences_1000000002694-01.pdf and are protected by the following copyright notice: Oligonucleotide sequences (c) 2016 Illumina, Inc. All rights reserved. Derivative works created by Illumina customers are authorized for use with Illumina instruments and products only. All other uses are strictly prohibited.
INDEXED
SINGLE_END
NEXTERA_V1
NEXTERA_V2
DUAL_INDEXED
FLUIDIGM
TRUSEQ_SMALLRNA
ALTERNATIVE_SINGLE_END

List[IlluminaAdapterPair] [INDEXED, DUAL_INDEXED, PAIRED_END]

--arguments_file

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

List[File] []

--COMPRESSION_LEVEL

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

int 5 [ [ -∞ ∞ ] ]

--CREATE_INDEX

Whether to create an index when writing VCF or coordinate sorted BAM output.

Boolean false

--CREATE_MD5_FILE

Whether to create an MD5 digest for any BAM or FASTQ files created.

boolean false

--FIVE_PRIME_ADAPTER

For specifying adapters other than standard Illumina

String null

--help / -h

display the help message

boolean false

--INPUT / -I

Undocumented option

R File null

--MAX_ERROR_RATE_PE

The maximum mismatch error rate to tolerate when clipping paired-end reads.

double 0.1 [ [ -∞ ∞ ] ]

--MAX_ERROR_RATE_SE

The maximum mismatch error rate to tolerate when clipping single-end reads.

double 0.1 [ [ -∞ ∞ ] ]

--MAX_RECORDS_IN_RAM

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 [ [ -∞ ∞ ] ]

--METRICS / -M

Histogram showing counts of bases_clipped in how many reads

R File null

--MIN_MATCH_BASES_PE

The minimum number of bases to match over (per-read) when clipping paired-end reads.

int 6 [ [ -∞ ∞ ] ]

--MIN_MATCH_BASES_SE

The minimum number of bases to match over when clipping single-end reads.

int 12 [ [ -∞ ∞ ] ]

--NUM_ADAPTERS_TO_KEEP

If pruning the adapter list, keep only this many adapter sequences when pruning the list (plus any adapters that were tied with the adapters being kept).

int 1 [ [ -∞ ∞ ] ]

--OUTPUT / -O

If output is not specified, just the metrics are generated

File null

--PAIRED_RUN / -PE

DEPRECATED. Whether this is a paired-end run. No longer used.

Boolean null

--PRUNE_ADAPTER_LIST_AFTER_THIS_MANY_ADAPTERS_SEEN / -APT

If looking for multiple adapter sequences, then after having seen this many adapters, shorten the list of sequences. Keep the adapters that were found most frequently in the input so far. Set to -1 if the input has a heterogeneous mix of adapters so shortening is undesirable.

int 100 [ [ -∞ ∞ ] ]

--QUIET

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

Boolean false

--REFERENCE_SEQUENCE / -R

Reference sequence file.

PicardHtsPath null

--showHidden / -showHidden

display hidden arguments

boolean false

--THREE_PRIME_ADAPTER

For specifying adapters other than standard Illumina

String null

--TMP_DIR

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

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

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

display the version number for this tool

boolean false

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GATK version 4.6.2.0 built at Sun, 13 Apr 2025 13:21:43 -0400.