@camerongenomics @pseudocistron Yup — but this is exactly how aligners have evolved over time. Even the ones intended to have the best fidelity to the spec don't do great here. Most don't have a good estimate of that (@BenLangmead's Q-tip was one attempt t
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@clintcodesbio @denizkural @OmicsOmicsBlog Just got reminded of this paper, other wise the BWA-MEM manuscript perhaps.
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@krsahlin @denizkural @BenLangmead's Qtip paper has nice discussions regarding MAPQ https://t.co/2wbPh1J3bj
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A tandem simulation framework for predicting mapping quality published as: https://t.co/2Vcbad0IBi @GenomeBiology #biorxiv