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

@author ktibbett@broadinstitute.org

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		The analysis directory for the binary output file.
--FLOWCELL_BARCODE -F		Flowcell barcode (e.g. 30PYMAAXX).
--INPUT -I		The BAM file to parse.
--OUTPUT_FILE_PREFIX		Prefix for all output files
--PAIRED_RUN -PE		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		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		Lane number.
--READ_CHUNK_SIZE -CHUNK	2000000	Number of reads to break into individual groups for alignment
--READ_NAME_PREFIX		Prefix to be stripped off the beginning of all read names (to make them short enough to run in Maq)
--READS_TO_ALIGN -NUM		Number of reads to align (null = all).
--RUN_BARCODE -RB		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 an index when writing VCF or coordinate sorted BAM output.
--CREATE_MD5_FILE	false	Whether to create an MD5 digest for any BAM or FASTQ files created.
--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		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

The analysis directory for the binary output file.

R File null

--arguments_file

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

List[File] []

--BASES_TO_WRITE

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

Whether to clip adapters from the reads

boolean true

--COMPRESSION_LEVEL

Compression level for all compressed files created (e.g. BAM and VCF).

int 5 [ [ -∞ ∞ ] ]

--CREATE_INDEX

Whether to create an index when writing VCF or coordinate sorted BAM output.

Boolean false

--CREATE_MD5_FILE

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

--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

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

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

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

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

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

String null

--READS_TO_ALIGN / -NUM

Number of reads to align (null = all).

Integer null

--REFERENCE_SEQUENCE / -R

Reference sequence file.

PicardHtsPath 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

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

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

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

display the version number for this tool

boolean false

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GATK version 4.6.2.0 built at Sun, 13 Apr 2025 13:21:43 -0400.