Details on how Picard-Tools define duplicate reads

fa8@sanger.ac.ukfa8@sanger.ac.uk Sanger InstituteMember

Dear colleagues,

I am trying to implement a script to group duplicate reads into families and would like to understand which criteria Picard's MarkDuplicates uses. I've read that it compares the 5' ends of reads (either single-end or paired-end), but haven't found much more. Is there any page or publication where these details are provided?

Thanks!

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