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_SEQUENCIAL_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.

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

---

Category Read Data Manipulation

---

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_SEQUENCIAL_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.

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	null	Input fastq file (optionally gzipped) for single end data, or first read in paired end data.
--OUTPUT  -O	null	Output SAM/BAM file.
--SAMPLE_NAME  -SM	null	Sample name to insert into the read group header
Optional Tool Arguments
--ALLOW_AND_IGNORE_EMPTY_LINES	false	Allow (and ignore) empty lines
--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	null	Inserted into the read group header
--FASTQ2  -F2	null	Input fastq file (optionally gzipped) for the second read of paired end data.
--help  -h	false	display the help message
--LIBRARY_NAME  -LB	null	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	null	The platform type (e.g. ILLUMINA, SOLID) to insert into the read group header
--PLATFORM_MODEL  -PM	null	Platform model to insert into the group header (free-form text providing further details of the platform/technology used)
--PLATFORM_UNIT  -PU	null	The platform unit (often run_barcode.lane) to insert into the read group header
--PREDICTED_INSERT_SIZE  -PI	null	Predicted median insert size, to insert into the read group header
--PROGRAM_GROUP  -PG	null	Program group to insert into the read group header.
--QUALITY_FORMAT  -V	null	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 this value is not specified, the quality format will be detected automatically.
--READ_GROUP_NAME  -RG	A	Read group name
--RUN_DATE  -DT	null	Date the run was produced, to insert into the read group header
--SEQUENCING_CENTER  -CN	null	The sequencing center from which the data originated
--SORT_ORDER  -SO	queryname	The sort order for the output sam/bam file.
--USE_SEQUENTIAL_FASTQS	false	Use sequential fastq files with the suffix _###.fastq or _###.fastq.gz.The files should be named: _001., _002., ..., _XYZ. The base files should be: _001. An example would be: RUNNAME_S8_L005_R1_001.fastq RUNNAME_S8_L005_R1_002.fastq RUNNAME_S8_L005_R1_003.fastq RUNNAME_S8_L005_R1_004.fastq RUNNAME_S8_L005_R1_001.fastq should be provided as FASTQ.
--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
Deprecated Arguments
--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.

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.

---

--ALLOW_AND_IGNORE_EMPTY_LINES / NA

Allow (and ignore) empty lines

Boolean  false

---

--arguments_file / NA

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

List[File]  []

---

--COMMENT / -CO

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

List[String]  []

---

--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

---

--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 File  null

---

--FASTQ2 / -F2

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

File  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

---

--LIBRARY_NAME / -LB

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

String  null

---

--MAX_Q / NA

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 / 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  [ [ -∞  ∞ ] ]

---

--MIN_Q / NA

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

int  0  [ [ -∞  ∞ ] ]

---

--OUTPUT / -O

Output SAM/BAM file.

R File  null

---

--PLATFORM / -PL

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

String  null

---

--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

---

--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 this value is not specified, the quality format will be detected automatically.

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

Solexa

Illumina

Standard

FastqQualityFormat  null

---

--QUIET / NA

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

Boolean  false

---

--READ_GROUP_NAME / -RG

Read group name

String  A

---

--REFERENCE_SEQUENCE / -R

Reference sequence file.

File  null

---

--RUN_DATE / -DT

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

Iso8601Date  null

---

--SAMPLE_NAME / -SM

Sample name to insert into the read group header

R String  null

---

--SEQUENCING_CENTER / -CN

The sequencing center from which the data originated

String  null

---

--showHidden / -showHidden

display hidden arguments

boolean  false

---

--SORT_ORDER / -SO

The sort order for the output sam/bam 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

---

--STRIP_UNPAIRED_MATE_NUMBER / NA

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

---

--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

---

--USE_SEQUENTIAL_FASTQS / NA

Use sequential fastq files with the suffix _###.fastq or _###.fastq.gz.The files should be named: _001., _002., ..., _XYZ. The base files should be: _001. An example would be: RUNNAME_S8_L005_R1_001.fastq RUNNAME_S8_L005_R1_002.fastq RUNNAME_S8_L005_R1_003.fastq RUNNAME_S8_L005_R1_004.fastq RUNNAME_S8_L005_R1_001.fastq should be provided as FASTQ.

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 4.1.3.0 built at Sat, 23 Nov 2019 16:20:54 -0500.