FastqToSam (picard 2.18.2 API)

java.lang.Object
- picard.cmdline.CommandLineProgram
- - picard.sam.FastqToSam

```
@DocumentedFeature
public class FastqToSam
extends CommandLineProgram
```
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 
 
```

Field Summary

Fields
Modifier and Type	Field	Description
`Boolean`	`ALLOW_AND_IGNORE_EMPTY_LINES`
`List<String>`	`COMMENT`
`String`	`DESCRIPTION`
`File`	`FASTQ`
`File`	`FASTQ2`
`String`	`LIBRARY_NAME`
`int`	`MAX_Q`
`int`	`MIN_Q`
`File`	`OUTPUT`
`String`	`PLATFORM`
`String`	`PLATFORM_MODEL`
`String`	`PLATFORM_UNIT`
`Integer`	`PREDICTED_INSERT_SIZE`
`String`	`PROGRAM_GROUP`
`htsjdk.samtools.util.FastqQualityFormat`	`QUALITY_FORMAT`
`String`	`READ_GROUP_NAME`
`htsjdk.samtools.util.Iso8601Date`	`RUN_DATE`
`String`	`SAMPLE_NAME`
`String`	`SEQUENCING_CENTER`
`htsjdk.samtools.SAMFileHeader.SortOrder`	`SORT_ORDER`
`Boolean`	`STRIP_UNPAIRED_MATE_NUMBER`	Deprecated.
`boolean`	`USE_SEQUENTIAL_FASTQS`

Fields inherited from class picard.cmdline.CommandLineProgram
COMPRESSION_LEVEL, CREATE_INDEX, CREATE_MD5_FILE, GA4GH_CLIENT_SECRETS, MAX_RECORDS_IN_RAM, QUIET, REFERENCE_SEQUENCE, referenceSequence, specialArgumentsCollection, TMP_DIR, USE_JDK_DEFLATER, USE_JDK_INFLATER, VALIDATION_STRINGENCY, VERBOSITY

Constructor Summary

Constructors
Constructor Description

FastqToSam()

Constructors
Constructor	Description
`FastqToSam()`

Method Summary

All Methods Static Methods Instance Methods Concrete Methods
Modifier and Type	Method	Description
`htsjdk.samtools.SAMFileHeader`	`createSamFileHeader()`	Creates a simple header with the values provided on the command line.
`protected String[]`	`customCommandLineValidation()`	Put any custom command-line validation in an override of this method.
`static htsjdk.samtools.util.FastqQualityFormat`	`determineQualityFormat(htsjdk.samtools.fastq.FastqReader reader1, htsjdk.samtools.fastq.FastqReader reader2, htsjdk.samtools.util.FastqQualityFormat expectedQuality)`	Looks at fastq input(s) and attempts to determine the proper quality format Closes the reader(s) by side effect
`protected int`	`doPaired(htsjdk.samtools.fastq.FastqReader freader1, htsjdk.samtools.fastq.FastqReader freader2, htsjdk.samtools.SAMFileWriter writer)`	More complicated method that takes two fastq files and builds pairing information in the SAM.
`protected int`	`doUnpaired(htsjdk.samtools.fastq.FastqReader freader, htsjdk.samtools.SAMFileWriter writer)`	Creates a simple SAM file from a single fastq file.
`protected int`	`doWork()`	Do the work after command line has been parsed.
`protected static List<File>`	`getSequentialFileList(File baseFastq)`	Get a list of FASTQs that are sequentially numbered based on the first (base) fastq.
`static void`	`main(String[] argv)`	Stock main method.
`void`	`makeItSo(htsjdk.samtools.fastq.FastqReader reader1, htsjdk.samtools.fastq.FastqReader reader2, htsjdk.samtools.SAMFileWriter writer)`	Handles the FastqToSam execution on the FastqReader(s).

Methods inherited from class picard.cmdline.CommandLineProgram
getCommandLine, getCommandLineParser, getDefaultHeaders, getFaqLink, getMetricsFile, getStandardUsagePreamble, getStandardUsagePreamble, getVersion, hasWebDocumentation, instanceMain, instanceMainWithExit, makeReferenceArgumentCollection, parseArgs, requiresReference, setDefaultHeaders, useLegacyParser

Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

FASTQ

@Argument(shortName="F1",
          doc="Input fastq file (optionally gzipped) for single end data, or first read in paired end data.")
public File FASTQ

FASTQ2

@Argument(shortName="F2",
          doc="Input fastq file (optionally gzipped) for the second read of paired end data.",
          optional=true)
public File FASTQ2

USE_SEQUENTIAL_FASTQS

@Argument(doc="Use sequential fastq files with the suffix <prefix>_###.fastq or <prefix>_###.fastq.gz",
          optional=true)
public boolean USE_SEQUENTIAL_FASTQS

QUALITY_FORMAT

@Argument(shortName="V",
          doc="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.",
          optional=true)
public htsjdk.samtools.util.FastqQualityFormat QUALITY_FORMAT

OUTPUT

@Argument(doc="Output SAM/BAM file. ",
          shortName="O")
public File OUTPUT

READ_GROUP_NAME

@Argument(shortName="RG",
          doc="Read group name")
public String READ_GROUP_NAME

SAMPLE_NAME

@Argument(shortName="SM",
          doc="Sample name to insert into the read group header")
public String SAMPLE_NAME

LIBRARY_NAME

@Argument(shortName="LB",
          doc="The library name to place into the LB attribute in the read group header",
          optional=true)
public String LIBRARY_NAME

PLATFORM_UNIT

@Argument(shortName="PU",
          doc="The platform unit (often run_barcode.lane) to insert into the read group header",
          optional=true)
public String PLATFORM_UNIT

PLATFORM

@Argument(shortName="PL",
          doc="The platform type (e.g. illumina, solid) to insert into the read group header",
          optional=true)
public String PLATFORM

SEQUENCING_CENTER

@Argument(shortName="CN",
          doc="The sequencing center from which the data originated",
          optional=true)
public String SEQUENCING_CENTER

PREDICTED_INSERT_SIZE

@Argument(shortName="PI",
          doc="Predicted median insert size, to insert into the read group header",
          optional=true)
public Integer PREDICTED_INSERT_SIZE

PROGRAM_GROUP

@Argument(shortName="PG",
          doc="Program group to insert into the read group header.",
          optional=true)
public String PROGRAM_GROUP

PLATFORM_MODEL

@Argument(shortName="PM",
          doc="Platform model to insert into the group header (free-form text providing further details of the platform/technology used)",
          optional=true)
public String PLATFORM_MODEL

COMMENT

@Argument(doc="Comment(s) to include in the merged output file\'s header.",
          optional=true,
          shortName="CO")
public List<String> COMMENT

DESCRIPTION

@Argument(shortName="DS",
          doc="Inserted into the read group header",
          optional=true)
public String DESCRIPTION

RUN_DATE

@Argument(shortName="DT",
          doc="Date the run was produced, to insert into the read group header",
          optional=true)
public htsjdk.samtools.util.Iso8601Date RUN_DATE

SORT_ORDER

@Argument(shortName="SO",
          doc="The sort order for the output sam/bam file.")
public htsjdk.samtools.SAMFileHeader.SortOrder SORT_ORDER

MIN_Q

@Argument(doc="Minimum quality allowed in the input fastq.  An exception will be thrown if a quality is less than this value.")
public int MIN_Q

MAX_Q

@Argument(doc="Maximum quality allowed in the input fastq.  An exception will be thrown if a quality is greater than this value.")
public int MAX_Q

STRIP_UNPAIRED_MATE_NUMBER

@Deprecated
@Argument(doc="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.")
public Boolean STRIP_UNPAIRED_MATE_NUMBER

Deprecated.

ALLOW_AND_IGNORE_EMPTY_LINES

@Argument(doc="Allow (and ignore) empty lines")
public Boolean ALLOW_AND_IGNORE_EMPTY_LINES

Constructor Detail
- FastqToSam
```
public FastqToSam()
```

Method Detail
- determineQualityFormat
```
public static htsjdk.samtools.util.FastqQualityFormat determineQualityFormat(htsjdk.samtools.fastq.FastqReader reader1,
                                                                             htsjdk.samtools.fastq.FastqReader reader2,
                                                                             htsjdk.samtools.util.FastqQualityFormat expectedQuality)
```
  Looks at fastq input(s) and attempts to determine the proper quality format Closes the reader(s) by side effect
  
  Parameters:
  
  reader1 - The first fastq input
  
  reader2 - The second fastq input, if necessary. To not use this input, set it to null
  
  expectedQuality - If provided, will be used for sanity checking. If left null, autodetection will occur
- main
```
public static void main(String[] argv)
```
  Stock main method.
- getSequentialFileList
```
protected static List<File> getSequentialFileList(File baseFastq)
```
  Get a list of FASTQs that are sequentially numbered based on the first (base) fastq. 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 where `baseFastq` is the first in that list.
- doWork
```
protected int doWork()
```
  Description copied from class: CommandLineProgram
  
  Do the work after command line has been parsed. RuntimeException may be thrown by this method, and are reported appropriately.
  
  Specified by:
  
  doWork in class CommandLineProgram
  
  Returns:
  
  program exit status.
- makeItSo
```
public void makeItSo(htsjdk.samtools.fastq.FastqReader reader1,
                     htsjdk.samtools.fastq.FastqReader reader2,
                     htsjdk.samtools.SAMFileWriter writer)
```
  Handles the FastqToSam execution on the FastqReader(s). In some circumstances it might be useful to circumvent the command line based instantiation of this class, however note that there is no handholding or guardrails to running in this manner. It is the caller's responsibility to close the reader(s)
  
  Parameters:
  
  reader1 - The FastqReader for the first fastq file
  
  reader2 - The second FastqReader if applicable. Pass in null if only using a single reader
  
  writer - The SAMFileWriter where the new SAM file is written
- doUnpaired
```
protected int doUnpaired(htsjdk.samtools.fastq.FastqReader freader,
                         htsjdk.samtools.SAMFileWriter writer)
```
  Creates a simple SAM file from a single fastq file.
- doPaired
```
protected int doPaired(htsjdk.samtools.fastq.FastqReader freader1,
                       htsjdk.samtools.fastq.FastqReader freader2,
                       htsjdk.samtools.SAMFileWriter writer)
```
  More complicated method that takes two fastq files and builds pairing information in the SAM.
- createSamFileHeader
```
public htsjdk.samtools.SAMFileHeader createSamFileHeader()
```
  Creates a simple header with the values provided on the command line.
- customCommandLineValidation
```
protected String[] customCommandLineValidation()
```
  Description copied from class: CommandLineProgram
  
  Put any custom command-line validation in an override of this method. clp is initialized at this point and can be used to print usage and access argv. Any options set by command-line parser can be validated.
  
  Overrides:
  
  customCommandLineValidation in class CommandLineProgram
  
  Returns:
  
  null if command line is valid. If command line is invalid, returns an array of error message to be written to the appropriate place.

Class FastqToSam

Inputs

Output

Usage examples

Example 1:

Example 2:

Field Summary

Fields inherited from class picard.cmdline.CommandLineProgram

Constructor Summary

Method Summary

Methods inherited from class picard.cmdline.CommandLineProgram

Methods inherited from class java.lang.Object

Field Detail

FASTQ

FASTQ2

USE_SEQUENTIAL_FASTQS

QUALITY_FORMAT

OUTPUT

READ_GROUP_NAME

SAMPLE_NAME

LIBRARY_NAME

PLATFORM_UNIT

PLATFORM

SEQUENCING_CENTER

PREDICTED_INSERT_SIZE

PROGRAM_GROUP

PLATFORM_MODEL

COMMENT

DESCRIPTION

RUN_DATE

SORT_ORDER

MIN_Q

MAX_Q

STRIP_UNPAIRED_MATE_NUMBER

ALLOW_AND_IGNORE_EMPTY_LINES

Constructor Detail

FastqToSam

Method Detail

determineQualityFormat

main

getSequentialFileList

doWork

makeItSo

doUnpaired

doPaired

createSamFileHeader

customCommandLineValidation