FastqToSam (Picard)

Converts a FASTQ file to an unaligned BAM or SAM file.

Output read records will contain the original base calls and quality scores will be translated depending on the base quality score encoding: FastqSanger, FastqSolexa and FastqIllumina.

There are also arguments to provide values for SAM header and read attributes that are not present in FASTQ (e.g see RG or SM below).

Inputs

One FASTQ file name for single-end or two for pair-end sequencing input data. These files might be in gzip compressed format (when file name is ending with ".gz").

Alternatively, for larger inputs you can provide a collection of FASTQ files indexed by their name (see USE_SEQUENTIAL_FASTQ for details below).

By default, this tool will try to guess the base quality score encoding. However you can indicate it explicitly using the QUALITY_FORMAT argument, and must do so if inputs are not a regular file (e.g. stdin).

Output

A single unaligned BAM or SAM file. By default, the records are sorted by query (read) name.

Usage examples

Example 1:

Single-end sequencing FASTQ file conversion. All reads are annotated as belonging to the "rg0013" read group that in turn is part of the sample "sample001".

java -jar picard.jar FastqToSam \
        F1=input_reads.fastq \
        O=unaligned_reads.bam \
        SM=sample001 \
        RG=rg0013

Example 2:

Similar to example 1 above, but for paired-end sequencing.

java -jar picard.jar FastqToSam \
       F1=forward_reads.fastq \
       F2=reverse_reads.fastq \
       O=unaligned_read_pairs.bam \
       SM=sample001 \
       RG=rg0013

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Category Read Data Manipulation

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Overview

Converts a FASTQ file to an unaligned BAM or SAM file.

Output read records will contain the original base calls and quality scores will be translated depending on the base quality score encoding: FastqSanger, FastqSolexa and FastqIllumina.

There are also arguments to provide values for SAM header and read attributes that are not present in FASTQ (e.g see RG or SM below).

Inputs

One FASTQ file name for single-end or two for pair-end sequencing input data. These files might be in gzip compressed format (when file name is ending with ".gz").

Alternatively, for larger inputs you can provide a collection of FASTQ files indexed by their name (see USE_SEQUENTIAL_FASTQ for details below).

By default, this tool will try to guess the base quality score encoding. However you can indicate it explicitly using the QUALITY_FORMAT argument, and must do so if inputs are not a regular file (e.g. stdin).

Output

A single unaligned BAM or SAM file. By default, the records are sorted by query (read) name.

Usage examples

Example 1:

Single-end sequencing FASTQ file conversion. All reads are annotated as belonging to the "rg0013" read group that in turn is part of the sample "sample001".

 java -jar picard.jar FastqToSam \
      F1=input_reads.fastq \
      O=unaligned_reads.bam \
      SM=sample001 \
      RG=rg0013
 

Example 2:

Similar to example 1 above, but for paired-end sequencing.

 java -jar picard.jar FastqToSam \
      F1=forward_reads.fastq \
      F2=reverse_reads.fastq \
      O=unaligned_read_pairs.bam \
      SM=sample001 \
      RG=rg0013
 

FastqToSam (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
--FASTQ  -F1		Input fastq file (optionally gzipped) for single end data, or first read in paired end data.
--OUTPUT  -O		Output BAM/SAM/CRAM file.
--SAMPLE_NAME  -SM		Sample name to insert into the read group header
Optional Tool Arguments
--ALLOW_AND_IGNORE_EMPTY_LINES	false	Allow (and ignore) empty lines
--ALLOW_EMPTY_FASTQ	false	Allow empty input fastq
--arguments_file		read one or more arguments files and add them to the command line
--COMMENT  -CO		Comment(s) to include in the merged output file's header.
--DESCRIPTION  -DS		Inserted into the read group header
--FASTQ2  -F2		Input fastq file (optionally gzipped) for the second read of paired end data.
--help  -h	false	display the help message
--LIBRARY_NAME  -LB		The library name to place into the LB attribute in the read group header
--MAX_Q	93	Maximum quality allowed in the input fastq. An exception will be thrown if a quality is greater than this value.
--MIN_Q	0	Minimum quality allowed in the input fastq. An exception will be thrown if a quality is less than this value.
--PLATFORM  -PL		The platform type (e.g. ILLUMINA, SOLID) to insert into the read group header
--PLATFORM_MODEL  -PM		Platform model to insert into the group header (free-form text providing further details of the platform/technology used)
--PLATFORM_UNIT  -PU		The platform unit (often run_barcode.lane) to insert into the read group header
--PREDICTED_INSERT_SIZE  -PI		Predicted median insert size, to insert into the read group header
--PROGRAM_GROUP  -PG		Program group to insert into the read group header.
--QUALITY_FORMAT  -V		A value describing how the quality values are encoded in the input FASTQ file. Either Solexa (phred scaling + 66), Illumina (phred scaling + 64) or Standard (phred scaling + 33). If input is from a regular file and this value is not specified, the quality format will be detected automatically. If input is not from a regular file, this value is required.
--READ_GROUP_NAME  -RG	A	Read group name
--RUN_DATE  -DT		Date the run was produced, to insert into the read group header
--SEQUENCING_CENTER  -CN		The sequencing center from which the data originated
--SORT_ORDER  -SO	queryname	The sort order for the output BAM/SAM/CRAM file.
--STRIP_UNPAIRED_MATE_NUMBER	false	Deprecated (No longer used). If true and this is an unpaired fastq any occurrence of '/1' or '/2' will be removed from the end of a read name.
--USE_SEQUENTIAL_FASTQS	false	Use sequential fastq files with the suffix _###.fastq[.gz]. The files should be named: _001., _002., ..., _XYZ. Use the *first* file for the --FASTQ argument, e.g., --FASTQ _001.. If paired end, use the *first* read2 file for the --FASTQ2 argument, e.g., _001.. Example: combine and convert 4 single end fastqs with filenames: RUNNAME_S8_L005_R1_001.fastq RUNNAME_S8_L005_R1_002.fastq RUNNAME_S8_L005_R1_003.fastq RUNNAME_S8_L005_R1_004.fastq Run command with --FASTQ RUNNAME_S8_L005_R1_001.fastq --USE_SEQUENTIAL_FASTQS true
--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.

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--ALLOW_AND_IGNORE_EMPTY_LINES

Allow (and ignore) empty lines

Boolean  false

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--ALLOW_EMPTY_FASTQ

Allow empty input fastq

Boolean  false

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--arguments_file

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

List[File]  []

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--COMMENT / -CO

Comment(s) to include in the merged output file's header.

List[String]  []

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--COMPRESSION_LEVEL

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

int  5  [ [ -∞  ∞ ] ]

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--CREATE_INDEX

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

Boolean  false

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--CREATE_MD5_FILE

Whether to create an MD5 digest for any BAM or FASTQ files created.

boolean  false

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--DESCRIPTION / -DS

Inserted into the read group header

String  null

---

--FASTQ / -F1

Input fastq file (optionally gzipped) for single end data, or first read in paired end data.

R PicardHtsPath  null

---

--FASTQ2 / -F2

Input fastq file (optionally gzipped) for the second read of paired end data.

PicardHtsPath  null

---

--help / -h

display the help message

boolean  false

---

--LIBRARY_NAME / -LB

The library name to place into the LB attribute in the read group header

String  null

---

--MAX_Q

Maximum quality allowed in the input fastq. An exception will be thrown if a quality is greater than this value.

int  93  [ [ -∞  ∞ ] ]

---

--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  [ [ -∞  ∞ ] ]

---

--MIN_Q

Minimum quality allowed in the input fastq. An exception will be thrown if a quality is less than this value.

int  0  [ [ -∞  ∞ ] ]

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--OUTPUT / -O

Output BAM/SAM/CRAM file.

R File  null

---

--PLATFORM / -PL

The platform type (e.g. ILLUMINA, SOLID) to insert into the read group header

String  null

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--PLATFORM_MODEL / -PM

Platform model to insert into the group header (free-form text providing further details of the platform/technology used)

String  null

---

--PLATFORM_UNIT / -PU

The platform unit (often run_barcode.lane) to insert into the read group header

String  null

---

--PREDICTED_INSERT_SIZE / -PI

Predicted median insert size, to insert into the read group header

Integer  null

---

--PROGRAM_GROUP / -PG

Program group to insert into the read group header.

String  null

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--QUALITY_FORMAT / -V

A value describing how the quality values are encoded in the input FASTQ file. Either Solexa (phred scaling + 66), Illumina (phred scaling + 64) or Standard (phred scaling + 33). If input is from a regular file and this value is not specified, the quality format will be detected automatically. If input is not from a regular file, this value is required.

The --QUALITY_FORMAT argument is an enumerated type (FastqQualityFormat), which can have one of the following values:

Solexa

Illumina

Standard

FastqQualityFormat  null

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--QUIET

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

Boolean  false

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--READ_GROUP_NAME / -RG

Read group name

String  A

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--REFERENCE_SEQUENCE / -R

Reference sequence file.

PicardHtsPath  null

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--RUN_DATE / -DT

Date the run was produced, to insert into the read group header

Iso8601Date  null

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--SAMPLE_NAME / -SM

Sample name to insert into the read group header

R String  null

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--SEQUENCING_CENTER / -CN

The sequencing center from which the data originated

String  null

---

--showHidden / -showHidden

display hidden arguments

boolean  false

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--SORT_ORDER / -SO

The sort order for the output BAM/SAM/CRAM file.

The --SORT_ORDER argument is an enumerated type (SortOrder), which can have one of the following values:

unsorted

queryname

coordinate

duplicate

unknown

SortOrder  queryname

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--STRIP_UNPAIRED_MATE_NUMBER

Deprecated (No longer used). If true and this is an unpaired fastq any occurrence of '/1' or '/2' will be removed from the end of a read name.

Boolean  false

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--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

---

--USE_SEQUENTIAL_FASTQS

Use sequential fastq files with the suffix _###.fastq[.gz]. The files should be named: _001., _002., ..., _XYZ. Use the *first* file for the --FASTQ argument, e.g., --FASTQ _001.. If paired end, use the *first* read2 file for the --FASTQ2 argument, e.g., _001.. Example: combine and convert 4 single end fastqs with filenames: RUNNAME_S8_L005_R1_001.fastq RUNNAME_S8_L005_R1_002.fastq RUNNAME_S8_L005_R1_003.fastq RUNNAME_S8_L005_R1_004.fastq Run command with --FASTQ RUNNAME_S8_L005_R1_001.fastq --USE_SEQUENTIAL_FASTQS true

boolean  false

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--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

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--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

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--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.