Set the mapping quality of reads with a given value to another given value
java -jar GenomeAnalysisTK.jar -T PrintReads -R reference.fasta -I input.bam -o output.file -rf ReassignOneMappingQuality -RMQF 255 -RMQT 60
| Argument name(s) | Default value | Summary | |
|---|---|---|---|
| Optional Parameters | |||
| --reassign_mapping_quality_from  -RMQF | 255 | Original mapping quality | |
| --reassign_mapping_quality_to  -RMQT | 60 | Desired mapping quality | |