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.
Convert CombineVariant output to individual vcf files
I was curious if it possible to convert the output of CombineVariants back into individual sample vcf files. Based on answered questions in other threads, I am under the impression that you should not try to use VariantFiltration on a combined output if variants were not called on an previously merged file. Is that correct? If so, could I basically reverse CombineVariants after using SelectVariants to analyze samples individually?
Also, I would like to point out that that all the links to the "Tools documentation index" are broken and displaying 404. I am not if you are aware.