Bam2sam step

This step allow to convert a BAM file into a SAM file.

  • Internal name: bam2sam
  • Available: Both local and distributed mode

  • Input port:
    • input: data to convert (in BAM format)

  • Output ports:
    • bam: converted data (in SAM format)


  • Mandatory parameter: None

  • Optional parameter:
    • Parameter Type Description Default value
    hadoop.reducer.task.count integer The count of Hadoop reducer tasks to use for this step. This parameter is only used in Hadoop mode Not set
  • Configuration example:
    • <!-- Convert BAM to SAM step -->
<step id="mybam2samstep" skip="false" discardoutput="false">
	<module>bam2sam</module>
	<parameters/>
</step>