What does the -A "Matching score" and -B "Mismatch penalty" flags doing in BWA mem?
0
1
Entering edit mode
5.4 years ago
beausoleilmo ▴ 440

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 • 2.9k views
ADD COMMENT

Login before adding your answer.

Traffic: 875 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6