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.
Its mentioned in the VQSR documentation that in order to achieve the best results, we need to call variants with at least 30 samples each time and then apply VQSR on the whole dataset. In our lab we only multiplex 4 exome samples in a run. Does this mean that for every single run I need to add 26 additional exome samples and call variants and then apply VQSR to the entire data set? Is it not recommended to run VQSR on single exome VCF file? Are there any other options for me ? (except hard filtering of variants)