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.
at which step to merge multiple samples
I have multiple fastq files for 1 individual (you can think of those files as replicates). I was wondering at which point in the GATK variant calling pipeline should I combine them to get the best results. I am looking for 1 set of variants present in that individual (1 vcf is desired). Should I combine them in the HC step?