Convert SAM or BAM files to FASTQ format
Author: Picard
Contact: gp-help@broadinstitute.org
Algorithm Version:
Summary
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/.
Parameters
| 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:
any
Operating System:
any
Language:
Java
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 |