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Mapping quality: bad and normal #239
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According to https://academic.oup.com/bioinformatics/article/25/14/1754/225615, MQ > 20 is good enough:
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Hello!
Dear authors, could you provide some kind of borders for the mapping quality
bwa-mem2
produces?Here (http://www.acgt.me/blog/2015/3/17/more-madness-with-mapq-scores-aka-why-bioinformaticians-hate-poor-and-incomplete-software-documentation#:~:text=BWA%20generates%20MAPQ%20scores%20between,mapping%20quality%20was%20not%20available) it is said that BWA generates MAPQ scores between 0–37.
What score should be treated as 'normal' for 30X WGS? And what is some kind of lower bound?
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