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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.
Truth or control samples - Variant calling
Are we able to incorporate truth/control samples in addition to dbSNP when calling variants with GVCF (cohorts) or the traditional way with HaplotypeCaller. There are for example situations where the sequences are for Australian, E Asian, or African samples, and we would like to include truth/control samples for those areas, perhaps from 1000 genomes or some other source.
If possible, what arguments do we use.