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.
merging bam files for an individual
I'm running HaplotypeCaller in GVCF mode, followed by GenotypeGVCF. For some individuals, I have more than one aligned bam file. Do I need to combine the individual's bam files in HaplotypeCaller to produce one GVCF, or can I produce multiple GVCFs per individual and combine them in GenotypeGVCF?