Computational Genomics Engineer — Variant Calling & Population Genetics

Summary

5 years designing variant calling and population-scale genomics platforms for clinical and research settings. Built a WDL/Cromwell pipeline processing 50,000 whole genomes at Regeneron. Strong software engineering background — rewrote a legacy VCF annotation tool in Rust, achieving 12× throughput improvement. Comfortable owning infrastructure (GCP, Terraform) end-to-end.

Experience

Genomics Software Engineer — Regeneron Genetics Center (2022–Present)

• Maintained and extended WDL pipelines running on GCP Life Sciences; processed 50k WGS samples for UK Biobank collaboration.
• Rewrote VEP annotation post-processing in Rust; reduced wall time from 6h to 28min per cohort (12× speedup).
• Implemented Hail-based GWAS QC framework; reduced analyst setup time from days to hours.
• Led adoption of Terraform for GCP infrastructure-as-code across 4-person team.

Bioinformatics Analyst — University Hospital Zürich (2020–2022)

• Built clinical-grade somatic variant calling pipeline (GATK Mutect2 + DeepVariant ensemble) with CAP/CLIA-ready reporting.
• Developed PostgreSQL schema and REST API for variant interpretation database used by 12 oncologists.

Selected Projects

• vcf-annotate-rs — open-source Rust crate for high-throughput VCF functional annotation (GitHub, 340 stars).
• hail-qc-toolkit — opinionated GWAS QC library wrapping Hail with sensible defaults; used by 3 academic labs.

Code Quality Notes

All repositories use conventional commits, semantic versioning, and automated releases. WDL pipelines have womtool validation in CI. Rust crates maintain >90% test coverage with criterion benchmarks. Infrastructure changes go through Terraform plan review in GitHub PRs before apply.