Purpose

Extracts read sequences and qualities from the input SAM/BAM dataset and outputs them in Sanger fastq format. In the RE_REVERSE=True mode (default behavior), if the read is aligned and the alignment is to the reverse strand on the genome, the read's sequence from input SAM.BAM dataset will be reverse-complemented prior to writing it to fastq in order restore correctly the original read sequence as it was generated by the sequencer.

Dataset collections - processing large numbers of datasets at once

This will be added shortly

Inputs, outputs, and parameters

Either a SAM file or a BAM file must be supplied. Galaxy automatically coordinate-sorts all uploaded BAM files.

From Picard documentation( http://broadinstitute.github.io/picard/):

FASTQ=File
F=File                        Output fastq file (single-end fastq or, if paired, first end of the pair fastq).
                              Required.

SECOND_END_FASTQ=File
F2=File                       Output fastq file (if paired, second end of the pair fastq).  Default value: null.


UNPAIRED_FASTQ=File
FU=File                       Output fastq file for unpaired reads; may only be provided in paired-fastq mode  Default
                              value: null.

RE_REVERSE=Boolean
RC=Boolean                    Re-reverse bases and qualities of reads with negative strand flag set before writing them
                              to fastq  Default value: true. Possible values: {true, false}

INTERLEAVE=Boolean
INTER=Boolean                 Will generate an interleaved fastq if paired, each line will have /1 or /2 to describe
                              which end it came from  Default value: false. Possible values: {true, false}

INCLUDE_NON_PF_READS=Boolean
NON_PF=Boolean                Include non-PF reads from the SAM file into the output FASTQ files. PF means 'passes
                              filtering'. Reads whose 'not passing quality controls' flag is set are non-PF reads.
                              Default value: false. Possible values: {true, false}

CLIPPING_ATTRIBUTE=String
CLIP_ATTR=String              The attribute that stores the position at which the SAM record should be clipped  Default
                              value: null.

CLIPPING_ACTION=String
CLIP_ACT=String               The action that should be taken with clipped reads: 'X' means the reads and qualities
                              should be trimmed at the clipped position; 'N' means the bases should be changed to Ns in
                              the clipped region; and any integer means that the base qualities should be set to that
                              value in the clipped region.  Default value: null.

READ1_TRIM=Integer
R1_TRIM=Integer               The number of bases to trim from the beginning of read 1.  Default value: 0.

READ1_MAX_BASES_TO_WRITE=Integer
R1_MAX_BASES=Integer          The maximum number of bases to write from read 1 after trimming. If there are fewer than
                              this many bases left after trimming, all will be written.  If this value is null then all
                              bases left after trimming will be written.  Default value: null.

READ2_TRIM=Integer
R2_TRIM=Integer               The number of bases to trim from the beginning of read 2.  Default value: 0.

READ2_MAX_BASES_TO_WRITE=Integer
R2_MAX_BASES=Integer          The maximum number of bases to write from read 2 after trimming. If there are fewer than
                              this many bases left after trimming, all will be written.  If this value is null then all
                              bases left after trimming will be written.  Default value: null.

INCLUDE_NON_PRIMARY_ALIGNMENTS=Boolean
                              If true, include non-primary alignments in the output.  Support of non-primary alignments
                              in SamToFastq is not comprehensive, so there may be exceptions if this is set to true and
                              there are paired reads with non-primary alignments.  Default value: false.
                              Possible values: {true, false}

Additional information

Additional information about Picard tools is available from Picard web site at http://broadinstitute.github.io/picard/ .