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.
See related forum discussion here. To see a list of annotation modules currently available from the GATK4 codebase, see here.
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