Added -M flag to BWA MEM for picard compatibility.
Added -M flag to BWA MEM for picard compatibility.

churchlab/millstone,woodymit/millstone_accidental_source,woodymit/millstone,woodymit/millstone_accidental_source,woodymit/millstone,churchlab/millstone,woodymit/millstone_accidental_source,churchlab/millstone,churchlab/millstone,woodymit/millstone,woodymit/millstone,woodymit/millstone_accidental_source