What does the -A "Matching score" and -B "Mismatch penalty" flags doing in BWA mem?
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7.3 years ago
beausoleilmo ▴ 580

In the manual, it's talking about "XM" as the

Number of mismatches in the alignment

But I find no places talking about this in the manual. The only thing that could influence this XM are the -A "Matching score" or -B "Mismatch penalty". But I don't know what they do.

Is the a way, using bwa mem to set the number of mismatches in the alignment to say a maximum of 5?

BWA Matching score penalty GWAS • 3.3k views
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