Sam2bam module

This module allow to convert a SAM file into a BAM file and create a BAI file. The alignments in the output BAM file are sorted by leftmost coordinates.

  • Internal name: sam2bam
  • Available: Both local and distributed mode

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

  • Output ports:
    • bam: converted data (in BAM format)
    • bai: index of the BAM file (in BAI format)


  • Mandatory parameter: None

  • Optional parameter:
    • Parameter Type Description Default value
    compression.level integer The level of compression in the 0-9 range. 5
    max.entries.in.ram integer The maximal number of BAM entries to store in memory. By lowering the value of this parameter out of memory errors can be avoided for long reads. 500000
    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:
    • <!-- Create BAMs step -->
<step id="mysam2bamstep" skip="false" discardoutput="false">
	<module>sam2bam</module>
	<parameters>
		<parameter>
			<name>compression.level</name>
			<value>5</value>
		</parameter>
	</parameters>
</step>