Filter alignments module

This module allow to filter the output alignments in SAM format.

WARNING : the filters order in the workflow file is not trivial. The output file of this module is the same, regardless the filters order. Nevertheless, informations in the log file depend of the filters order.

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

  • Input port:
    • input: alignments in SAM format (format: mapper_results_sam)

  • Output port:
    • output: alignments in SAM format (format: mapper_results_sam)

  • Optional parameters:
    • Parameter Type Description Default value
    removeunmapped None If enabled, remove unmapped reads. N/A
    removemultimatches None If enabled, remove all alignments of a multi-matches read. N/A
    removesecondary None If enabled, remove all alignment with "secondary alignment" flag. N/A
    removesupplementary None If enabled, remove all alignment with "supplementary alignment" flag. N/A
    keeponematch None If enabled, keep only the first alignment of a multi-matches read. N/A
    quality.threshold integer The threshold for the mapping quality. All the alignments with a mapping quality lower to the threshold will be removed. Not set
    keepnumbermatch.threshold int Keep the given number of the first alignments for a read. Not set
    distancefromreference.threshold int Keep alignments of a read according to the distance of the read from the reference sequence on the genome. This filter is useful to detect SNP and indel. Not set
    gsnapfilter None If enabled, remove alignments that are not supported by the expression estimation module, that is multiple alignments and those that contain a splice event. N/A
    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:
    • <!-- SAM filter step -->
<step skip="false" discardoutput="true">
	<module>filtersam</module>
	<parameters>
		<parameter>
			<name>removeunmapped</name>
			<value>true</value>
		</parameter>
		<parameter>
			<name>removemultimatches</name>
			<value>true</value>
		</parameter>
	</parameters>
</step>