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.
Regarding Different genotypes for same sample using Unified Genotyper & Haplotype Caller
I am doing multi sample cohort exome analysis for which i have called SNPs using both callers (UG & HC).For one of my important SNP, i am observing different genotypes in few samples from both the callers.
Which to rely upon for further analysis???