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Set the mapping quality of all reads to a given value

Category Read Filters


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).

See also

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)


BAM file(s) with the mapping qualities of all reads reassigned to the specified value

Usage example

  java -jar GenomeAnalysisTK.jar \
      -T PrintReads \
      -R reference.fasta \
      -I input.bam \
      -o output.file \
      -rf ReassignMappingQuality \
      -DMQ 35

Command-line Arguments

ReassignMappingQualityFilter specific arguments

This table summarizes the command-line arguments that are specific to this tool. For more details on each argument, see the list further down below the table or click on an argument name to jump directly to that entry in the list.

Argument name(s) Default value Summary
Optional Parameters
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

Default read mapping quality to assign to all reads

int  60  [ [ -∞  ∞ ] ]

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GATK version 3.6-0-g89b7209 built at 2017/02/09 12:52:48.