Hi all, I forgot to use the -M option in bwa mem. But it's too late to find out. I don't want to rerun all my analyses from the bwa mem to variant calling cuz this will take another week. I read in other discussion that Picard was fixed to be able to recoginize the flag 0*800-0*900 for secondary alignment and so on in new versions. So I just want to confirm if it makes no difference for Picard to recognize those flags from bwa mem outputs without the -M option! I wish it's not necessary to run everything all over again by adding the -M option to bwa mem. Thank you, Lisa
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