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.
GenotypeGVCFs output with additional annotation
Thank you guys for developing & maintaining such a good software!
I'm actually just starting to use GATK with Haplotypecaller. For me, there's a very useful annotation "StrandBiasBySample" or "StrandAlleleCountsBySample" that gives all the alignment information for a variant. It can be generated by HC, but after joint genotyping, it's just gone.
There is a previous post asking about how to add this annotation to the final vcf, and Sheila mentioned she's already put in a request for adding this.
So I'm just wandering, have you guys fixed this in one of the nighty build?