If you happen to see a question you know the answer to, please do chime in and help your fellow community members. We encourage our fourm members to be more involved, jump in and help out your fellow researchers with their questions. GATK forum is a community forum and helping each other with using GATK tools and research is the cornerstone of our success as a genomics research community.We appreciate your help!

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.
We will be out of the office on November 11th and 13th 2019, due to the U.S. holiday(Veteran's day) and due to a team event(Nov 13th). We will return to monitoring the GATK forum on November 12th and 14th respectively. Thank you for your patience.

MarkDuplicates policy on reads that are unaligned/unmapped?

Our bams are created according to the "lossless" alignment procedure described in this article. The procedure involves mixing unaligned and aligned reads with Picard's MergeBamAlignment. So they contain both mapped and unmapped reads. These bams are then sorted with SortSam - so that the sort order in the header becomes:

@HD VN:1.6 SO:coordinate

On such bams, is there any special sort order that should be specified with MarkDuplicates to reduce memory usage, or speedup processing? Can you recommend --ASSUME_SORT_ORDER X ? It's not clear from the documentation how MarkDuplicates handles reads that don't have reliable position information in the bam.


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