created by shlee
on 2017-11-27
Variant annotations are available to HaplotypeCaller, Mutect2, VariantAnnotator and GenotypeGVCFs. These are listed under Annotations in the [Tool Documentation](https://software.broadinstitute.org/gatk/documentation/tooldocs/current/).
- 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](https://gatkforums.broadinstitute.org/gatk/discussion/8726/why-dp-in-format-filed-cant-be-re-annotate-base-on-input-bam-file-by-variantannotator). To see a list of annotation modules currently available from the GATK4 codebase, see [here](https://github.com/broadinstitute/gatk/tree/master/src/main/java/org/broadinstitute/hellbender/tools/walkers/annotator).
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Updated on 2017-12-22