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CollectIlluminaLaneMetrics (Picard)

Collects Illumina lane metrics for the given BaseCalling analysis directory. This tool produces quality control metrics on cluster density for each lane of an Illumina flowcell. This tool takes Illumina TileMetrics data and places them into directories containing lane- and phasing-level metrics. In this context, phasing refers to the fraction of molecules that fall behind or jump ahead (prephasing) during a read cycle.

Usage example:

java -jar picard.jar CollectIlluminaLaneMetrics \
RUN_DIR=test_run \
OUTPUT_DIRECTORY=Lane_output_metrics \
OUTPUT_PREFIX=experiment1 \
READ_STRUCTURE=25T8B25T

Please see the CollectIlluminaLaneMetrics definitions for a complete description of the metrics produced by this tool.


Category Base Calling


Overview

Command-line wrapper around IlluminaLaneMetricsCollector.

CollectIlluminaLaneMetrics (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
--OUTPUT_DIRECTORY
null The directory to which the output file will be written
--OUTPUT_PREFIX
 -O
null The prefix to be prepended to the file name of the output file; an appropriate suffix will be applied
--RUN_DIRECTORY
null The Illumina run directory of the run for which the lane metrics are to be generated
Optional Tool Arguments
--arguments_file
[] read one or more arguments files and add them to the command line
--FILE_EXTENSION
 -EXT
null Append the given file extension to all metric file names (ex. OUTPUT.illumina_lane_metrics.EXT). None if null
--help
 -h
false display the help message
--IS_NOVASEQ
false Boolean the determines if this run is a NovaSeq run or not. (NovaSeq tile metrics files are in cycle 25 directory.
--READ_STRUCTURE
 -RS
null A description of the logical structure of clusters in an Illumina Run, i.e. a description of the structure IlluminaBasecallsToSam assumes the data to be in. It should consist of integer/character pairs describing the number of cycles and the type of those cycles (B for Sample Barcode, M for molecular barcode, T for Template, and S for skip). E.g. If the input data consists of 80 base clusters and we provide a read structure of "28T8M8B8S28T" then the sequence may be split up into four reads: * read one with 28 cycles (bases) of template * read two with 8 cycles (bases) of molecular barcode (ex. unique molecular barcode) * read three with 8 cycles (bases) of sample barcode * 8 cycles (bases) skipped. * read four with 28 cycles (bases) of template The skipped cycles would NOT be included in an output SAM/BAM file or in read groups therein. If not given, will use the RunInfo.xml in the run directory.
--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.


--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


--FILE_EXTENSION / -EXT

Append the given file extension to all metric file names (ex. OUTPUT.illumina_lane_metrics.EXT). None if null

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


--IS_NOVASEQ / NA

Boolean the determines if this run is a NovaSeq run or not. (NovaSeq tile metrics files are in cycle 25 directory.

boolean  false


--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  [ [ -∞  ∞ ] ]


--OUTPUT_DIRECTORY / NA

The directory to which the output file will be written

R File  null


--OUTPUT_PREFIX / -O

The prefix to be prepended to the file name of the output file; an appropriate suffix will be applied

R String  null


--QUIET / NA

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

Boolean  false


--READ_STRUCTURE / -RS

A description of the logical structure of clusters in an Illumina Run, i.e. a description of the structure IlluminaBasecallsToSam assumes the data to be in. It should consist of integer/character pairs describing the number of cycles and the type of those cycles (B for Sample Barcode, M for molecular barcode, T for Template, and S for skip). E.g. If the input data consists of 80 base clusters and we provide a read structure of "28T8M8B8S28T" then the sequence may be split up into four reads: * read one with 28 cycles (bases) of template * read two with 8 cycles (bases) of molecular barcode (ex. unique molecular barcode) * read three with 8 cycles (bases) of sample barcode * 8 cycles (bases) skipped. * read four with 28 cycles (bases) of template The skipped cycles would NOT be included in an output SAM/BAM file or in read groups therein. If not given, will use the RunInfo.xml in the run directory.

ReadStructure  null


--REFERENCE_SEQUENCE / -R

Reference sequence file.

File  null


--RUN_DIRECTORY / NA

The Illumina run directory of the run for which the lane metrics are to be generated

R File  null


--showHidden / -showHidden

display hidden arguments

boolean  false


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