Picard.SamToFastq (v3)

Convert SAM or BAM files to FASTQ format

Author: Picard

Contact: gp-help@broadinstitute.org

Algorithm Version:


This module converts a file in SAM format (or its binary equivalent, BAM format) to FASTQ format. SAM is a standard short read alignment that allows aligners to attach custom tags to individual alignments. For more information on the SAM format, see the specification at http://samtools.sourceforge.net. For more information on the FASTQ format, see the FASTQ specification (http://maq.sourceforge.net/fastq.shtml). This module implements the SamToFastq function from Picard. For more information, see the Picard Web site: http://picard.sourceforge.net/.


Name Description
input file * The SAM or BAM file
per read group * Whether to output a fastq file per read group
re-reverse bases * Whether to re-reverse bases and qualities of reads with negative strand flag set
include non pf reads * Whether to include non-PF reads
clipping attribute Attribute that stores the position at which the SAM record should be clipped
clipping action Action to take with clipped reads when a clipping attribute is specified
clipping action quality value Value to set base qualities to when clipping action is "change base quality values"
fastq output prefix 1 The fastq output file name for single-end fastq or first end of a paired fastq. Only specify when "per read group" is "no".
fastq output prefix 2 The second end of a paired fastq. Only specify when "per read group" is "no".

* - required

Output Files

1. FASTQ file(s)
The number of FASTQ files depends on the options specified: if the SAM file is for paired-end reads and if the per read group parameter is set to yes. For more information on the FASTQ format, see the specification: http://maq.sourceforge.net/fastq.shtml.

Platform Dependencies

Task Type:
Data Format Conversion

CPU Type:

Operating System:


Version Comments

Version Release Date Description
3 2013-06-21 Fixed issue with choice parameters not appearing as drop downs
2 2012-08-07 Changed name from SamToFastq to Picard.SamToFastq