Test-drive the GATK tools and Best Practices pipelines on Terra
Check out this blog post to learn how you can get started with GATK and try out the pipelines in preconfigured workspaces (with a user-friendly interface!) without having to install anything.
single-end data and optical duplicates (Mark Duplicates)
I met a problem with MarkDuplicates: I tried to estimate optical duplicates with both single-end and paired end datasets.
In both cases, MarkDuplicates was able to detect duplicates and to mark them. However, in single-end datasets, it always says to me "Found 0 optical duplicate clusters" (I tested with several samples and several datasets -- I cannot believe there is 0 optical duplicates in all these samples). I tried Markduplicates in only 2 paired-end samples and each time it could detect optical duplicates (12% and 6% of optical duplicates among duplicates).
I really do not understand these results. Is there something I missed, like a parameter, or something?
For information, my data were sequenced on the Hiseq4000 and I followed this tutorial: http://gatkforums.broadinstitute.org/gatk/discussion/6747/how-to-mark-duplicates-with-markduplicates-or-markduplicateswithmatecigar
Thank you very much!