Why the RealignerTargetCreator list came out ot be different
I forgot to add the -M option when I started with bwa mem. So I reanalyzed one of my samples with the -M option in bwa mem and then continued with the downstream pipeline without any change to parameter setting. However, the list generated by 'RealignerTargetCreator' was a bit different (most of the positions were the same) this time. So with or without the -M option still made a difference on how Picard recognized the flags I guess? But how can that happen? Does that mean I have to do everything again from the bwa mem step? Anyway to rescue in the middle?