Principal Software Engineer - GATK

About the role

GATK, HTSJDK, and Picard are foundational infrastructure for the global genomics community - with tens of millions of downloads, tens of thousands of scientific citations, and a documented footprint across hundreds of clinical trials spanning cancer, ALS, and other diseases.

The Broad Institute is resuming dedicated development and active maintenance of all three packages, and we're hiring an experienced engineer to serve as a primary maintainer. You'll take broad ownership of the work needed to clear the file-format standards backlog, restore community confidence, and build a sustainable, decentralized contributor model - amplified by modern AI coding tools and an empowered community of contributors. This is a high-autonomy role with significant latitude to shape priorities, carrying ownership that was previously spread across a larger team.

The impact is real and immediate. Numerous computational groups across the Institute depend on this toolset to meet their commitments. You'll collaborate with both internal and external partners (such as those at the Wellcome Sanger Institute, EBI/ENA, Fulcrum, and across GA4GH).

What you'll do

The exact mix will flex with community and Institute needs, but the role generally spans:

Standards & development

• Advance file-format standards support across the toolset (for example, VCF 4.4), keeping the Java/JVM genomics ecosystem aligned with ratified GA4GH standards as they evolve.
• Author bug fixes and high-impact features across the repositories, upholding the engineering quality and test coverage that have kept these tools relevant for over a decade.

Release engineering & maintenance

• Drive a regular release cadence across the repositories, ensuring updates reach downstream channels.
• Triage issues and review pull requests, working down a substantial backlog and prioritizing high-impact internal and community needs.

Community, governance & communication

• Help establish and run a Trusted Developer Program - recruiting and onboarding external contributors, administering a tiered access model, and maintaining governance documentation.
• Support the user community, including monitoring and responding on the GATK forums.
• Represent the project at conferences and community meetings (e.g. GA4GH) and help align priorities across collaborators and Broad programs.

Tooling & acceleration

• Apply state-of-the-art AI/ML coding tools to accelerate review and development across large, complex, multi-language codebases.
• Over time, explore LLM-based tooling to help answer recurring community questions from existing documentation.

Early focus areas

Sequencing and timelines will be set with the hiring manager, but early work is likely to center on:

• Advancing priority standards work such as VCF 4.4.
• Standing up the Trusted Developer Program and re-establishing a regular release cadence.
• Actively updating the source repositories to modern AI-friendly standards.

What we're looking for

• Excellent written and verbal communication and a collaborative, community-facing disposition.
• Substantial professional software engineering experience building and maintaining production-grade systems.
• Typically requires 10+ years of related experience with Bachelor’s degree; or 8+ years with Master’s degree; or a PhD with 5+ years’ experience; or equivalent experience.
• Proficiency in Java/JVM languages or a demonstrated track record of becoming rapidly productive in a large, mature, multi-language codebase.
• Strong Python skills for tooling, analysis, and pipeline work.
• Experience writing, testing, and deploying bioinformatics workflows in WDL or NextFlow.
• Deep working knowledge of genomics/bioinformatics: sequencing data and core file formats (BAM/CRAM/VCF/BCF), variant representation, and large-callset processing.
• Demonstrated ownership of open-source or shared infrastructure, code review, release management, and sustaining quality in a codebase many others depend on.
• Experience designing or operating large-scale cloud data pipelines (GCP, AWS, or Azure).
• Comfort adopting AI-assisted development workflows.
• Interest in learning new technologies and programming languages, such as Rust.

Strongly preferred

• Prior hands-on experience with the GATK ecosystem (GATK / HTSJDK / Picard) or other Broad genomics infrastructure (GenomicsDB, Terra, GCS-based workflows).
• Familiarity with genomic file-format internals and compression (e.g., htslib, noodles).
• MLOps background and ML/AI pipeline tooling experience.
• Experience in regulated/GxP clinical or production environments.
• Engagement with GA4GH or other genomics standards bodies.

Tech environment

Java/JVM

• Python
• GitHub-based open-source workflow
• Docker
• GCP
• GA4GH file-format standards
• AI-assisted development tooling

The expected base pay range for this position as listed above is based on a 40 hour per week schedule. Broad provides pay ranges representing its reasonable and good faith estimate of what the organization reasonably expects to pay for a position at the time of posting. Actual compensation will vary based on factors including but not limited to, relevant skills, experience, education, qualifications, and other factors permissible by law.

At Broad, your base pay is just one part of a comprehensive total rewards package. From day one, this role offers a competitive benefits package including medical, dental, vision, life, and disability insurance; a 401(k) retirement plan; flexible spending and health savings accounts; at least 13 paid holidays; winter closure; paid time off; parental and family care leave; and an employee assistance program, among other Broad benefits.

The Broad Institute is an equal opportunity employer. All qualified applicants will receive consideration for employment without regard to race, national origin, religion, age, color, sex, disability, protected veteran status, or any other characteristic protected by local, state, or federal laws, rules, or regulations.

Should you need a reasonable accommodation to complete the application or interview process, please contact [email protected] for assistance.