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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.
Missing metrics for a sample with CollectVariantCallingMetrics
I am using CollectVariantCallingMetrics on vcf generated with GATK, version 188.8.131.52 and my Picard version is 2.1.0. Interestingly while my vcf has 4 samples, I got the metrics for only 3 samples. Am I missing something here? I did not error out while running the tool.