The -M option in bwa mem and reducereads

Lisa0508Lisa0508 Ann Arbor, MIMember

Dear all,
I know it's not a good place to ask my first question. But I am anxious to know the answer. If someone knows the answer, it will be greatly appreciated. I forgot to use the -M option in bwa mem on all my data sets. It will take another week if I rerun all steps from bwa mem to variant calling for each sample. In topics from earlier years, some people said that the downstream variant calling will be decreased in number without the -M option in bwa mem. But more recent years discussion said that Picard can recognize all those flags including the split alignment flags in sam files. Yet I got no error message in the 'MarkDuplicates' step by Picard. My first question is that 1. How different will the variant calling be with or without the -M option? If your answer is the -M option has to be added, I will have to run all my analyses from the beginning. So my second question is that 2. Is it good to use 'ReduceReads' to save some time for variant calling?
Thank you very much,
Lisa

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