A read filter (transformer) that sets all reads mapping quality to a given value.
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.
BAM file(s) with all reads mapping qualities reassigned
java -jar GenomeAnalysisTK.jar -rf ReassignMappingQuality -DMQ 35
This table summarizes the command-line arguments that are specific to this tool. For details, see the list further down below the table.
|--default_mapping_quality||int||60||Default read mapping quality to assign to all reads|
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 read mapping quality to assign to all reads.
GATK version 2.5-2-gdb4546e built at 2013/05/01 09:32:36.