What does the -A "Matching score" and -B "Mismatch penalty" flags doing in BWA mem?
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?
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