I have been testing the BWA-Picard-GATK pipeline today, and did not realize I should have set the -M option for bwa until I got error message when I use Picard to mark duplicate reads. It throws an exception, and I found a post saying that the "-M" should be set for bwa in order to make it compatible with Picard and GATK. So I am asking what value I should set for the -M option? what's the range of the alignment score?
-M INT Mismatch penalty. BWA will not search for suboptimal hits with a score lower than (bestScore-misMsc).