BamToBfq (Picard)

Converts a BAM file into a BFQ (binary fastq formatted) file.

The BFQ format is the input format to some tools like Maq aligner.

Input

A single BAM file to convert

Output

One or two FASTQ files depending on whether the BAM file contains single- or paired-end sequencing data. You must indicate the output directory that will contain these files (ANALYSIS_DIR) and the output file name prefix (OUTPUT_FILE_PREFIX).

Usage example:

java -jar picard.jar BamToBfq \
     I=input.bam \
     ANALYSIS_DIR=output_dir \
     OUTPUT_FILE_PREFIX=output_name \
     PAIRED_RUN=false

Category Read Data Manipulation

Overview

Converts a BAM file into a BFQ (binary fastq formatted) file.

The BFQ format is the input format to some tools like Maq aligner.

Input

A single BAM file to convert

Output

Usage example:

     java -jar picard.jar BamToBfq \
             I=input.bam \
             ANALYSIS_DIR=output_dir \
             OUTPUT_FILE_PREFIX=output_name \
             PAIRED_RUN=false

BamToBfq (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
--ANALYSIS_DIR	null	The analysis directory for the binary output file.
--FLOWCELL_BARCODE -F	null	Flowcell barcode (e.g. 30PYMAAXX).
--INPUT -I	null	The BAM file to parse.
--OUTPUT_FILE_PREFIX	null	Prefix for all output files
--PAIRED_RUN -PE	null	Whether this is a paired-end run.
Optional Tool Arguments
--arguments_file	[]	read one or more arguments files and add them to the command line
--BASES_TO_WRITE	null	The number of bases from each read to write to the bfq file. If this is non-null, then only the first BASES_TO_WRITE bases from each read will be written.
--CLIP_ADAPTERS	true	Whether to clip adapters from the reads
--help -h	false	display the help message
--INCLUDE_NON_PF_READS -NONPF	false	Whether to include non-PF reads
--LANE -L	null	Lane number.
--READ_CHUNK_SIZE -CHUNK	2000000	Number of reads to break into individual groups for alignment
--READ_NAME_PREFIX	null	Prefix to be stripped off the beginning of all read names (to make them short enough to run in Maq)
--READS_TO_ALIGN -NUM	null	Number of reads to align (null = all).
--RUN_BARCODE -RB	null	Deprecated option; use READ_NAME_PREFIX instead
--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.

--ANALYSIS_DIR / NA

The analysis directory for the binary output file.

R File null

--arguments_file / NA

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

List[File] []

--BASES_TO_WRITE / NA

The number of bases from each read to write to the bfq file. If this is non-null, then only the first BASES_TO_WRITE bases from each read will be written.

Integer null

--CLIP_ADAPTERS / NA

Whether to clip adapters from the reads

boolean true

--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

--FLOWCELL_BARCODE / -F

Flowcell barcode (e.g. 30PYMAAXX).

Exclusion: This argument cannot be used at the same time as OUTPUT_FILE_PREFIX.

R 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

--INCLUDE_NON_PF_READS / -NONPF

Whether to include non-PF reads

Boolean false

--INPUT / -I

The BAM file to parse.

R File null

--LANE / -L

Lane number.

Exclusion: This argument cannot be used at the same time as OUTPUT_FILE_PREFIX.

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_FILE_PREFIX / NA

Prefix for all output files

Exclusion: This argument cannot be used at the same time as FLOWCELL_BARCODE, LANE.

R String null

--PAIRED_RUN / -PE

Whether this is a paired-end run.

R Boolean null

--QUIET / NA

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

Boolean false

--READ_CHUNK_SIZE / -CHUNK

Number of reads to break into individual groups for alignment

Integer 2000000 [ [ -∞ ∞ ] ]

--READ_NAME_PREFIX / NA

Prefix to be stripped off the beginning of all read names (to make them short enough to run in Maq)

String null

--READS_TO_ALIGN / -NUM

Number of reads to align (null = all).

Integer null

--REFERENCE_SEQUENCE / -R

Reference sequence file.

File null

--RUN_BARCODE / -RB

Deprecated option; use READ_NAME_PREFIX instead

Exclusion: This argument cannot be used at the same time as READ_NAME_PREFIX.

String 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 4.0.11.0 built at 23-11-2018 02:11:49.