Hi, everyone!

I am new to the gatk pipelines, so I'm not sure is it necessary to use the -M option in the bwa men commond before I put the outcoming bam file to the gatk mutect pipelines for calling the mutation variants? I have read some post about the supplementary alignment and secondary alignment, I'm still confused, is there big difference between the gatk mutect pipelines whether I use the -M option or not, which one is recommended for gatk?

Thank you!!!