Hi everyone, I am recently using BWA-MEM for aligning human genome. I found that when a hit (hit A) with a higher score falls in a the extension of another hit (hit B) which computed previously, BWA-MEM doesn't do the extension for hit A. However, on the final output, BWA-MEM uses the alignment for hit A and score for hit B. I am confused on this problem.
Any inputs would be appreciated. Thanks!