MarkIlluminaAdapters (Picard)

Reads a SAM or BAM 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 a SAM file. The SAM/BAM 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

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
null Undocumented option
--METRICS
 -M
null 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
null 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
null If output is not specified, just the metrics are generated
--PAIRED_RUN
 -PE
null 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
null 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 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

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 / NA

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

int  30  [ [ -∞  ∞ ] ]


--ADAPTERS / NA

Which adapters sequences to attempt to identify and clip.

List[IlluminaAdapterPair]  [INDEXED, DUAL_INDEXED, PAIRED_END]


--arguments_file / NA

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

List[File]  []


--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


--FIVE_PRIME_ADAPTER / NA

For specifying adapters other than standard Illumina

String  null


--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

Undocumented option

R File  null


--MAX_ERROR_RATE_PE / NA

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

double  0.1  [ [ -∞  ∞ ] ]


--MAX_ERROR_RATE_SE / NA

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

double  0.1  [ [ -∞  ∞ ] ]


--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  [ [ -∞  ∞ ] ]


--METRICS / -M

Histogram showing counts of bases_clipped in how many reads

R File  null


--MIN_MATCH_BASES_PE / NA

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

int  6  [ [ -∞  ∞ ] ]


--MIN_MATCH_BASES_SE / NA

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

int  12  [ [ -∞  ∞ ] ]


--NUM_ADAPTERS_TO_KEEP / NA

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 / NA

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

Boolean  false


--REFERENCE_SEQUENCE / -R

Reference sequence file.

File  null


--showHidden / -showHidden

display hidden arguments

boolean  false


--THREE_PRIME_ADAPTER / NA

For specifying adapters other than standard Illumina

String  null


--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 4.0.0.0 built at 10-58-2018 11:58:10.