ReassignMappingQualityFilter

A read filter (transformer) that sets all reads mapping quality to a given value.

Category Read Filters

Overview

If a BAM file contains erroneous or missing mapping qualities, this 'filter' will set all your mapping qualities to a given value. Default being 60.

Input

BAM file(s)

Output

BAM file(s) with all reads mapping qualities reassigned

Examples

    java
      -jar GenomeAnalysisTK.jar
      -rf ReassignMappingQuality
      -DMQ 35

Command-line Arguments

ReassignMappingQualityFilter specific arguments

This table summarizes the command-line arguments that are specific to this tool. For details, see the list further down below the table.

Name	Type	Default value	Summary
Optional
--default_mapping_quality	int	60	Default read mapping quality to assign to all reads

Argument details

Arguments in this list are specific to this tool. Keep in mind that other arguments are available that are shared with other tools (e.g. command-line GATK arguments); see Inherited arguments above.

--default_mapping_quality / -DMQ ( int with default value 60 )

Default read mapping quality to assign to all reads.

GATK version 2.5-2-gdb4546e built at 2013/05/01 09:32:36.