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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.
I am trying to figure out the 'broad-prod-wgs-germline-snps-indels/PairedEndSingleSampleWf.gatk4.0.wdl' workflow posted on git hub.
I see that in MarkDuplicates task you assume that the bam is sorted by - queryname (ASSUME_SORT_ORDER="queryname"), but prior to this, in the SortSam task, you sort bam only by coordinates. (SORT_ORDER="coordinate" ).