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CheckIlluminaDirectory (Picard)

Asserts the validity for specified Illumina basecalling data.

This tool will check that the basecall directory and the internal files are available, exist, and are reasonably sized for every tile and cycle. Reasonably sized means non-zero sized for files that exist per tile and equal size for binary files that exist per cycle or per tile. If DATA_TYPES {Position, BaseCalls, QualityScores, PF, or Barcodes} are not specified, then the default data types used by IlluminaBasecallsToSam are used. CheckIlluminaDirectory DOES NOT check that the individual records in a file are well-formed.

Usage example:

java -jar picard.jar CheckIlluminaDirectory \
BASECALLS_DIR=/BaseCalls/ \
READ_STRUCTURE=25T8B25T \
LANES=1 \
DATA_TYPES=BaseCalls

Category Base Calling


Overview

Program to check a lane of an Illumina output directory. This program checks that files exist, are non-zero in length, for every tile/cycle and specified data type. If NO data type is specified then the default data types used by IlluminaBasecallsToSam are used.

CheckIlluminaDirectory (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 basecalls output directory.
--LANES
 -L
[] The number of the lane(s) to check.
--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. Note: If you want to check whether or not a future IlluminaBasecallsToSam or ExtractIlluminaBarcodes run will fail then be sure to use the exact same READ_STRUCTURE that you would pass to these programs for this run.
Optional Tool Arguments
--arguments_file
[] read one or more arguments files and add them to the command line
--DATA_TYPES
 -DT
[] The data types that should be checked for each tile/cycle. If no values are provided then the data types checked are those required by IlluminaBaseCallsToSam (which is a superset of those used in ExtractIlluminaBarcodes). These data types vary slightly depending on whether or not the run is barcoded so READ_STRUCTURE should be the same as that which will be passed to IlluminaBasecallsToSam. If this option is left unspecified then both ExtractIlluminaBarcodes and IlluminaBaseCallsToSam should complete successfully UNLESS the individual records of the files themselves are spurious.
--FAKE_FILES
 -F
false A flag to determine whether or not to create fake versions of the missing files.
--help
 -h
false display the help message
--LINK_LOCS
 -X
false A flag to create symlinks to the loc file for the X Ten for each tile.
--TILE_NUMBERS
 -T
[] The number(s) of the tile(s) to check.
--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]  []


--BASECALLS_DIR / -B

The basecalls output directory.

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


--DATA_TYPES / -DT

The data types that should be checked for each tile/cycle. If no values are provided then the data types checked are those required by IlluminaBaseCallsToSam (which is a superset of those used in ExtractIlluminaBarcodes). These data types vary slightly depending on whether or not the run is barcoded so READ_STRUCTURE should be the same as that which will be passed to IlluminaBasecallsToSam. If this option is left unspecified then both ExtractIlluminaBarcodes and IlluminaBaseCallsToSam should complete successfully UNLESS the individual records of the files themselves are spurious.

Set[IlluminaDataType]  []


--FAKE_FILES / -F

A flag to determine whether or not to create fake versions of the missing files.

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


--LANES / -L

The number of the lane(s) to check.

R List[Integer]  []


--LINK_LOCS / -X

A flag to create symlinks to the loc file for the X Ten for each tile.

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  [ [ -∞  ∞ ] ]


--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. Note: If you want to check whether or not a future IlluminaBasecallsToSam or ExtractIlluminaBarcodes run will fail then be sure to use the exact same READ_STRUCTURE that you would pass to these programs for this run.

R String  null


--REFERENCE_SEQUENCE / -R

Reference sequence file.

File  null


--showHidden / -showHidden

display hidden arguments

boolean  false


--TILE_NUMBERS / -T

The number(s) of the tile(s) to check.

List[Integer]  []


--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 4.0.3.0 built at 09-43-2018 09:43:10.