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.
Picard MarkDuplicates with UMI
In MarkDuplicates, how is the newly added UMI option specified? The documentation (https://broadinstitute.github.io/picard/command-line-overview.html ) refers to a BARCODE_TAG string option; should this value be the name of the bam tag used for storing the umi (e.g., if the umi tag is of the form bc:Z:ACTG, then this option should be set to "bc")?
Is there a standard bam tag name for the UMI barcode (BX?). It is my understanding "BC" (and the corresponding "QT" tag) refers to the sample barcode, is this correct