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.
I am currently unsure of how to interpret the output of GenotypeGVCFs when typing my ~600 samples.
Genotype format at a given locus with 2 alternate alleles:
--This is what I am expecting for each sample
Genotype format at another given locus with 2 alternate alleles:
--I really don't understand this
I have written several down-stream scripts which rely on this format being consistent -- why are there so many fields in some of these lines?
I apologize if this is very obvious and documented somewhere, but I have tried searching with no results.