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Check out the documentation at CombineDuplicates.
Can anyone comment on the availability of CombineDuplicates? I'm not finding it in the current GATK-lite download (2.1.3).
It's a private tool not available for public use. Sorry!
Eric Banks, PhD -- Senior Group Leader, MPG Analysis, Broad Institute of Harvard and MIT
I have read the CombineDuplicates documentation but I'm still not sure on what this tool does. I have targeted capture data with high coverage which means that I get a lot of dups that might not be PCR dups but rather the same sequence over and over due to high coverage. I'm looking for a tool that will go through my BAM file and keep one of a number of duplicate reads. Is this what CombineDuplicates does?
And could you please clarify what you mean by private tool, is this not included when the latest version of GATK is downloaded?
Correct, it's not available to users outside of the GATK development team (unfortunately some of the private tools got announced here accidentally).