Holiday Notice:
The Frontline Support team will be slow to respond December 17-18 due to an institute-wide retreat and offline December 22- January 1, while the institute is closed. Thank you for your patience during these next few weeks. Happy Holidays!

Variant annotations

shleeshlee CambridgeMember, Broadie, Moderator admin
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

Issue · Github
by shlee

Issue Number
2706
State
open
Last Updated
Sign In or Register to comment.