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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.
Recommendation / best practices GVCF GQ bands
Dear GATK team,
Do you have any recommendation or best practice guidelines on the GVCFGQBands setting? This used to be (gatk < 3.2) [0,5,20,60] but has been changed one block per GQ value in gatk > 3.3. We would like to decrease the file size of the g.vcf files without loosing to much resolution / sensitivity. In the gvcf docs the 'old' defaults are still mentioned: https://www.broadinstitute.org/gatk/guide/article?id=4017