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 basesMarkIlluminaAdapters (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
GATK version 4.0.9.0 built at 25-11-2019 01:11:10.
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