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Set the mapping quality of reads with a given value to another given value

Category Read Filters


This read transformer will change a certain read mapping quality to a different value without affecting reads that have other mapping qualities. This is intended primarily for users of RNA-Seq data handling programs such as TopHat, which use MAPQ = 255 to designate uniquely aligned reads. According to convention, 255 normally designates "unknown" quality, and most GATK tools automatically ignore such reads. By reassigning a different mapping quality to those specific reads, users of TopHat and other tools can circumvent this problem without affecting the rest of their dataset.

This differs from the ReassignMappingQuality filter by its selectivity -- only one mapping quality is targeted. ReassignMappingQuality will change ALL mapping qualities to a single one, and is typically used for datasets that have no assigned mapping qualities.


BAM file(s)


BAM file(s) with one read mapping quality selectively reassigned as desired

Usage example

    java -jar GenomeAnalysisTK.jar \
      -T PrintReads \
      -R reference.fasta \
      -I input.bam \
      -o output.file \
      -rf ReassignOneMappingQuality \
      -RMQF 255 \
      -RMQT 60

Command-line Arguments

ReassignOneMappingQualityFilter 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
255 Original mapping quality
60 Desired mapping quality

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.

--reassign_mapping_quality_from / -RMQF

Original mapping quality

int  255  [ [ -∞  ∞ ] ]

--reassign_mapping_quality_to / -RMQT

Desired mapping quality

int  60  [ [ -∞  ∞ ] ]

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