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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.
Input bam file for the CNN pipeline
I was looking to test the CNN pipeline and I saw that in the HC step was added the "-bamout" option (HC). To run the 2D model in the CNNScoreVariants tool I have to use as input bam file the original bam (post BQSR bam) or the bamout bam from the HC step?