I received some bams where duplicates were marked using Picard. I'd like to unmark all duplicate reads for a study we're doing. Does anyone know of an existing tool? I haven't found anything in google land.
If there isn't an existing tool, could you provide some guidance how to unmark them myself? I've read the SAM spec (http://samtools.github.io/hts-specs/SAMv1.pdf) and understand I need to change the bit flag, but I'm not sure the best way to approach it.