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Variant annotations

shleeshlee CambridgeMember, Broadie, Moderator
edited December 2017 in Dictionary

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.

Post edited by shlee on

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