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.
Sorry I'm not clear on one point:
Say I want to run VQSR on a set of 30 samples (exomes).
Do I need to run genotypeGVCFs on all 30 GVCF files, and then feed the single joint VCF
output into variantrecalibrator,
do I need to feed the 30 individual VCF files into variantrecalibrator?