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Picard MarkDuplicates Barcode Tag

CG_AndersonCG_Anderson Member
edited December 2019 in Ask the GATK team

I was wondering how the implementation of MarkDuplicates differs when the --barcode_tag option is specified and I haven't been able to find anything in my searches. I'm terribly sorry if this has been explained and I just haven't found it.

As I understand it MarkDuplicates tries to mark duplicates that stem from the same original DNA fragment (thus "Both tools identify duplicates as sets of read pairs that have the same unclipped alignment start and unclipped alignment end." [HowTo](https://software.broadinstitute.org/gatk/documentation/article?id=6747) So if barcodes such as 10X chromium are representative of an original fragment, will MarkDuplicates only mark a read pair as a duplicate if has the same start, end and barcode tag?



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