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Request: Offsetting the MappingQuality of the reads in a bam file?
Dear GATK team,
I noticed you offered an unsupported option for handling bam files with non-standard Mapping Qualities: e.g. "adding -rf ReassignMappingQuality -DMQ 60 to your command-line would change all mapping qualities in your bam to 60."
Could I make a request for an option to offset the mapping qualities, for example with -1 ? So that 255 -1 becomes 254 ? I do not want to reassign all my reads with one value, but rather, offset the values to preserve the differences in MQ.
The reason I propose this is that some of us use aligners like the STAR aligner, and in this case 255 is given to uniquely mapped reads (useful for programs like STAR/Tophat/Cufflniks). This breaks convention, I know, but it would be useful to offset the MQ in GATK rather than run an awk command and generate a separate bam file just for variant calling.