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VCF Parser

A VAST DataEngine serverless function that transforms raw VCF output into clinically enriched variant records.

What It Does

Triggered when a VCF file lands in the genomics-vcf-outputs bucket
Downloads and parses the VCF, extracting INFO fields (DP, AF, DVQ) and gene annotations
Queries ClinVar via MyVariant.info for clinical significance of each variant
For pathogenic variants, generates LLM-powered clinical summaries via NVIDIA NIM
Memoization: checks VastDB for known variants before making any external API calls — reuses cached descriptions and embeddings if already stored
Passes the enriched variant list to genomics-variant-processor via function chaining

Configure in deployments/dataengine-genomics-pipeline/genomics-ingest.yaml:

Key	Description
`use_api_catalog`	`true` = NVIDIA API Catalog, `false` = self-hosted NIM
`nvidia_api_key`	Required when `use_api_catalog: true`
`llm_model`	LLM model for variant summaries (default: `meta/llama-3.1-70b-instruct`)
`s3endpoint`	VAST S3 endpoint for VCF download

Trigger: S3 ObjectCreated on genomics-vcf-outputs (via Kafka topic genomics)
Input: VCF file at s3://genomics-vcf-outputs/{patient_id}/{sample_id}/{sample_id}.vcf
Output: Enriched variant list passed to genomics-variant-processor via chaining
Cache: Variants already in VastDB skip ClinVar and LLM calls entirely