Set the mapping quality of all reads 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 the mapping qualities of all reads reassigned to the specified value
java -jar GenomeAnalysisTK.jar \ -T PrintReads \ -R reference.fasta \ -I input.bam \ -o output.file \ -rf ReassignMappingQuality \ -DMQ 35
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|
|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
int 60 [ [ -∞ ∞ ] ]
GATK version 3.6-0-g89b7209 built at 2017/02/09 12:52:48.