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.
Extracting variants for multiple read groups with VariantsToTable
I have a VCF file representing several related individuals and I want to extract the information into a table using VariantsToTable. All I really need is the genotype for each individual in the set at each variant position. I've tried extracting with VariantsToTable but can't find a way to separate the different read groups in the output, or to get a simple text representation of the genotype at each position.
I can see all of the information I need when I load the file into IGV so I'm guessing there must be a simply way to do this that I'm missing?
Any help is much appreciated.