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
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
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
GATK version 4.1.2.0 built at Sat, 23 Nov 2019 17:42:42 -0500.
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