A read filter (transformer) that sets all reads mapping quality to a given value.
If a BAM file contains erroneous or missing mapping qualities (MAPQ), this read transformer will set all your mapping qualities to a given value (see arguments list for default value).
ReassignOneMappingQualityFilter: reassigns a single MAPQ value, as opposed to all those found in the BAM file.
Note that due to the order of operations involved in applying filters, it is possible that other read filters (determined either at command-line or internally by the tool you are using) will be applied to your data before this read transformation can be applied. If one of those other filters acts on the read mapping quality (MAPQ), then you may not obtain the expected results. Unfortunately it is currently not possible to change the order of operations from command line. To avoid the problem, we recommend applying this filter separately from any other analysis, using PrintReads.
BAM file(s) with all reads mapping qualities reassigned
java -jar GenomeAnalysisTK.jar \ -T PrintReads \ -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 2.8-1-g2a26ec9 built at 2013/12/06 16:54:02.