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.
Variant Annotation: PossibleDeNovo
I used the variant annotator on a multi sample vcf and I am happy to report that it worked great (especially being tree reducible). I had a question that I could not find in the documentation. For each variant call it the annotator would either declare a sample to be a "hiConfDeNovo" or a "loConfDeNovo" or there would be no assessment whatsover (indicating I suspect no De Novos for that variant call).
My question: What defines a "hiConfDeNovo" and what defines a "loConfDeNovo" as it is used by the annotator. If there was some documentation I had overlooked please let me know, otherwise any insight is much appreciated.
Thank you as always