Convert SAM or BAM files to FASTQ format
Author: Picard
Contact: gp-help@broadinstitute.org
Algorithm Version:
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
Task Type:
Data Format Conversion
CPU Type:
any
Operating System:
any
Language:
Java
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 |