java -jar GenomeAnalysisTK.jar -T PrintReads -R reference.fasta -I input.bam -o output.file -rf ReassignMappingQuality -DMQ 35
Argument name(s) | Default value | Summary | |
---|---|---|---|
Optional Parameters | |||
--default_mapping_quality  -DMQ | 60 | Default read mapping quality to assign to all reads |