Question: What does the -A "Matching score" and -B "Mismatch penalty" flags doing in BWA mem?
1
gravatar for beausoleilmo
3.4 years ago by
beausoleilmo300
McGill University
beausoleilmo300 wrote:

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?

gwas bwa penalty matching score • 2.2k views
ADD COMMENTlink written 3.4 years ago by beausoleilmo300
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