Showing tool doc from version 4.1.0.0 | The latest version is 4.1.4.0

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_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
--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

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


Return to top


See also General Documentation | Tool Docs Index Tool Documentation Index | Support Forum

GATK version 4.1.0.0 built at Wed, 30 Jan 2019 10:21:04 +0530.