Tagged with #mapping quality
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Comments (3)


I was wondering if GATK uses the MAPQ column in the sam file in any of its calculations?

Thanks! Stephanie

Comments (6)


I'm trying to call variants from bowtie-aligned reads, I used PrintReads with ReassignMappingQuality filter to give all reads a mapping score of 60 to replace default value of 255. However, I'm wondering if this assignment would introduce any bias in variant calling.

Thanks a lot!

Comments (4)

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.