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Request: Offsetting the MappingQuality of the reads in a bam file?

GermanLGermanL Member
edited February 2013 in Ask the GATK team

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.

Best Answer


  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie admin

    Is 255 the only quality that breaks convention? If so it would be better to handle it specifically rather than offset everything.

    Normally we would consider this to be the problem of whoever develops the tools that break convention. But if this is a feature that is widely used for RNA seq data, perhaps we can do something to special-case it. I'll look into it.

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie admin

    OK, I've added your feature request to my todo list. It's not high priority right now so I can't give you an ETA of when it will happen, but I'll let you know when it's done.

  • GermanLGermanL Member

    Thank you for adding this feature to the wish list. I think it will broaden the appeal to users of RNA-seq data and future proof GATK for compatibility with other tools.

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