At a Glance
- Tasks: Lead the development of essential genomics tools and collaborate with global partners.
- Company: Join the Broad Institute, a leader in genomics research and innovation.
- Benefits: Enjoy competitive pay, comprehensive health benefits, and flexible work options.
- Other info: Dynamic hybrid work environment with opportunities for professional growth.
- Why this job: Make a real impact in genomics while working with cutting-edge technology.
- Qualifications: 10+ years in software engineering with strong Java and Python skills.
The predicted salary is between 44550 - 54450 £ per year.
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
- 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 prioritising 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 centre 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
Principal Software Engineer - GATK in Cambridge employer: Broad Institute
The Broad Institute is an exceptional employer, offering a dynamic work environment in Cambridge, MA, where innovation meets collaboration. As a Clinical Genomics Coordinator, you will be part of a mission-driven team dedicated to advancing precision medicine through cutting-edge genomic research, with ample opportunities for professional growth and development. Enjoy a comprehensive benefits package, a supportive work culture, and the chance to contribute to impactful projects that shape the future of healthcare.
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We think you need these skills to ace Principal Software Engineer - GATK in Cambridge
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Show off your coding skills:When applying for a software engineering role, it's super important to showcase your coding skills. Make sure your CV includes your tech stack, any relevant programming languages you’re comfortable with, and examples of projects you've worked on. If you have a GitHub profile, link it up! We love to see code in action.
Tailor your portfolio:For a full-time role, we’d expect to see some solid examples of your work in your portfolio. Make sure to include at least two or three projects that highlight your problem-solving skills and your ability to work with different technologies. Focus on the projects that are most relevant to the position at Broad Institute.
Craft a killer cover letter:Your cover letter is your chance to stand out—make it personal! Explain why you want to work at Broad Institute and how your skills align with the role. Show us your passion for software development. We dig enthusiastic candidates who understand the value of collaboration and continuous learning!
Be clear and concise:When it comes to writing your CV and cover letter, clarity is key. Avoid jargon that could confuse us and stick to simple, direct language. Highlight your achievements with quantifiable results where possible, and keep everything easy to read. A well-organised application goes a long way!
How to prepare for a job interview at Broad Institute
✨Brush Up on Your Coding Skills
For a full-time software engineering role, it's crucial that we stay sharp with our coding abilities. Expect technical questions that might involve solving problems on the spot or discussing algorithms. Practise on platforms like LeetCode or HackerRank to get comfortable with the types of questions that often come up.
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Make sure we’re well-acquainted with the tools and technologies listed in the job description. Familiarise ourselves with any specific frameworks or programming languages mentioned. If Broad Institute uses React or Node.js, for instance, be ready to discuss how we’ve used them in previous projects or coursework.
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Bring along a portfolio that highlights our best work. This could be code samples, GitHub repositories, or any side projects we’ve built. Make sure we can talk through our thought process for each project, especially the challenges we faced and how we solved them—this shows our problem-solving skills in action.
✨Prepare for Behavioural Questions
While technical skills are key, full-time positions also require cultural fit. Be ready to discuss our previous experiences and how we handle teamwork, conflict, and deadlines. Brush up on the STAR method—Situation, Task, Action, Result—to clearly articulate our past experiences when discussing how we've contributed to a team.
