README.md

annotations

Repository for VEP annotations and "extra" annotations.

Each v0.x is associated with a published Dockstore workflow.

vepAnnotateHail_v0.1.wdl: https://dockstore.org/workflows/github.com/talkowski-lab/annotations/vep-annotate-hail-v01

• Relatively stable. Currently uses VEP v112 but TODO: edit so using different VEP version inputs only involves changing a few WDL inputs.
• Plugins:
  • AlphaMissense
  • EVE

vepAnnotateHailMT_v0.1.wdl: https://dockstore.org/workflows/github.com/talkowski-lab/annotations/vep-annotate-hail-mt-v01

• Relatively stable. Basically replicates vepAnnotateHail_v0.1.wdl but expects MT input and saves as MT (TODO: maybe output as VCF?).
• Rarely used, only if we have input in MT form and not VCF(s).

vepAnnotateHailHT_v0.1.wdl: https://dockstore.org/workflows/github.com/talkowski-lab/annotations/vep-annotate-hail-ht-v01

• Relatively stable. Basically replicates vepAnnotateHail_v0.1.wdl but expects HT input and saves as HT.
• Used for any tabular input (supplementary tables, excel sheets, TSVs, HTs, etc.).

vepAnnotateHailNIFS_v0.1.wdl: https://dockstore.org/workflows/github.com/talkowski-lab/annotations/vep-annotate-hail-NIFS-v01

• Main difference with vepAnnotateHail_v0.1.wdl are the RemoveRawMutectCalls and addHGVScGeneSymbolField tasks.

vepAnnotateHailExtra_v0.1.wdl: https://dockstore.org/workflows/github.com/talkowski-lab/annotations/vep-annotate-hail-extra-v01

• Potentially misleading name because VEP is not run, but this workflow is intended to be run after vep-annotate-hail-v(x.x) for "extra" annotations:
  • [Optional] Noncoding (from bed file)
  • LOEUF from gnomAD v2 and gnomAD v4
  • OMIM
  • REVEL
  • MPC
  • ClinVar
  • [Optional] Gene list(s)
  • [Optional] SpliceAI
• v0.1: annotate with only one (optional) gene list.
• v0.2: annotate with any number of (optional) gene lists.

TODO: Generally want to add scripts to the Docker images for each task/workflow instead of having them as WDL inputs, but not a priority.