Add VEP + LOFTEE (+ GERP + HGNC) to VAT [VS-1520] [VS-1765] [VS-1767]

[mcovarr]

Almost successful run, failing only on the (unsurprising) difference in table size.

Dockerfile PR here, though ultimately we would probably want to keep this in the Variants repo.

[Copilot]

Pull request overview

This PR integrates VEP (Variant Effect Predictor) and LOFTEE (Loss-Of-Function Transcript Effect Estimator) annotations into the Variant Annotations Table (VAT), adding support for GERP conservation scores and HGNC gene nomenclature data. The implementation creates a new Docker image for VEP+LOFTEE and establishes a pipeline to generate, load, and process these annotations through BigQuery.

Key changes:

• Adds VEP+LOFTEE annotation generation task with GERP and HGNC support
• Implements BigQuery pipeline for loading and transforming raw VEP+LOFTEE output
• Updates VAT schema with new fields: hgnc_symbol, hgnc_id, LoF annotations, and GERP scores

Reviewed changes

Copilot reviewed 5 out of 5 changed files in this pull request and generated 2 comments.

Show a summary per file

File	Description
scripts/variantstore/wdl/GvsUtils.wdl	Adds vep_loftee_docker image reference and updates variants_docker version
scripts/variantstore/variant-annotations-table/GvsCreateVATfromVDS.wdl	Implements VEP+LOFTEE annotation workflow with three new tasks and integrates results into VAT
scripts/variantstore/scripts/variant_annotation_table/schema/vat_schema.json	Adds schema definitions for HGNC and LOFTEE annotation fields
scripts/variantstore/scripts/variant_annotation_table/schema/variant_transcript_schema.json	Adds schema definitions for HGNC and LOFTEE annotation fields
.dockstore.yml	Updates branch tracking configuration

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[gbggrant]

Looks good to me.

[gatk-bot]

Github actions tests reported job failures from actions build 19713361580
Failures in the following jobs:

Test Type	JDK	Job ID	Logs
conda	17.0.6+10	19713361580.3	logs