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# Principal Software Engineer - GATK

- **Company:** Broad Institute
- **Location:** Somerville, MA, United States
- **Experience:** Expert
- **Salary:** $150,000 - $210,000
- **Contract:** Permanent contract
- **Skills:** Java (Programming Language), Artificial Intelligence, Amazon Web Services, Microsoft Azure, Code Review, Github, Java Virtual Machine (JVM), Python (Programming Language), Open Source Technology, Release Management, Simple Data Format, Software Engineering, Large Language Models, Codebase, Machine Learning Operations, Data Pipelines, GXP, Docker, Programming Languages
- **Published:** November 7, 2026
- **Apply:** https://www.juju.com/job/7_5B15BC8C6FF4EF00480E665789B7A8B0

## About the Role

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

## Description

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