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 annotations are available to HaplotypeCaller, Mutect2, VariantAnnotator and GenotypeGVCFs. These are listed under Annotations in the Tool Documentation.
- HaplotypeCaller and Mutect2 calculate annotations based on realigned reads.
- If given the optional BAM input, VariantAnnotator will calculate annotations based on the pileup. Otherwise, VariantAnnotator and GenotypeGVCFs calculate summary metrics based on existing VCF fields.
- Some annotations, when called by different tools, may give different results.
Post edited by shlee on