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CollectIlluminaBasecallingMetrics (Picard)

Collects Illumina Basecalling metrics for a sequencing run.

This tool will produce per-barcode and per-lane basecall metrics for each sequencing run. Mean values for each metric are determined using data from all of the tiles. This tool requires the following data, LANE(#), BASECALLS_DIR, READ_STRUCTURE, and an input file listing the sample barcodes. Program will provide metrics including: the total numbers of bases, reads, and clusters, as well as the fractions of each bases, reads, and clusters that passed Illumina quality filters (PF) both per barcode and per lane. For additional information on Illumina's PF quality metric, please see the corresponding GATK Dictionary entry.

The input barcode_list.txt file is a file containing all of the sample and molecular barcodes and can be obtained from the ExtractIlluminaBarcodes tool.

Note: Metrics labeled as percentages are actually expressed as fractions!

Usage example:

java -jar picard.jar CollectIlluminaBasecallingMetrics \
BASECALLS_DIR=/BaseCalls/ \
LANE=001 \
READ_STRUCTURE=25T8B25T \
INPUT=barcode_list.txt

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


Category Base Calling


Overview

A Command line tool to collect Illumina Basecalling metrics for a sequencing run Requires a Lane and an input file of Barcodes to expect. Outputs metrics:
  • Mean Clusters Per Tile
  • Standard Deviation of Clusters Per Tile
  • Mean Pf Clusters Per Tile
  • Standard Deviation of Pf Clusters Per Tile
  • Mean Percentage of Pf Clusters Per Tile
  • Standard Deviation of Percentage of Pf Clusters Per Tile

CollectIlluminaBasecallingMetrics (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
--BASECALLS_DIR
 -B
null The Illumina basecalls output directory from which data are read
--LANE
 -L
null The lane whose data will be read
--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.
Optional Tool Arguments
--arguments_file
[] read one or more arguments files and add them to the command line
--BARCODES_DIR
 -BCD
null The barcodes directory with _barcode.txt files (generated by ExtractIlluminaBarcodes). If not set, use BASECALLS_DIR.
--help
 -h
false display the help message
--INPUT
 -I
null The file containing barcodes to expect from the run - barcodeData.#
--OUTPUT
 -O
null The file to which the collected metrics are written
--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]  []


--BARCODES_DIR / -BCD

The barcodes directory with _barcode.txt files (generated by ExtractIlluminaBarcodes). If not set, use BASECALLS_DIR.

File  null


--BASECALLS_DIR / -B

The Illumina basecalls output directory from which data are read

R File  null


--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


--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

The file containing barcodes to expect from the run - barcodeData.#

File  null


--LANE / -L

The lane whose data will be read

R Integer  null


--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 / -O

The file to which the collected metrics are written

File  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.

R String  null


--REFERENCE_SEQUENCE / -R

Reference sequence file.

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.