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.
VariantAnnotator requirements for some annotations
I found that VariantAnnotator sometimes does not annotate some annotations that are requested.
A ) The Rank Sum Test annotations MQRankSum & BaseQRankSum
I was not able to identify the requirements that have to be met, so they are being calculated for a variant.
B ) InbreedingCoeff
This one seems to be connected to the number of total called alleles (AN).
For me there needed to be at least 10% alleles be called (19/186).
The doc for that says  "at least 10 founder samples". Maybe this has to be updated to 10%?
These are the ones I observed.
Can someone tell me more about that?