{"id":578845,"url":"https://alion.io/job/broad-institute-principal-software-engineer-gatk","title":"Principal Software Engineer - GATK","company":{"id":15717,"name":"Broad Institute","domain":"broadinstitute.org","url":"https://alion.io/company/broad-institute","size_band":"501-1000","is_staffing_agency":false,"employer_type":"direct","is_intermediary":false,"listed_via":null,"ats_vendor":"Avature","truth_index":null},"role":"Backend","role_family":"Backend","seniority":"lead","employment_type":null,"work_mode":"on_site","remote_scope":null,"remote_scope_basis":null,"remote_working_hours":null,"hiring_geo_confidence":"structured","locations":["Cambridge, United States"],"countries":["US"],"hiring_countries":[],"hiring_countries_total":0,"salary":null,"salary_estimate":{"min_usd":148000,"max_usd":295000,"period":"year","method":"role_seniority_country_remote_cell","sample_n":1231},"experience_years_min":10,"visa_sponsorship":false,"relocation_package":false,"has_equity":false,"technologies":[{"name":"AWS","optional":false},{"name":"Azure","optional":false},{"name":"GCP","optional":false},{"name":"Java","optional":false},{"name":"LLM","optional":false},{"name":"Python","optional":false},{"name":"Rust","optional":false},{"name":"Docker","optional":true},{"name":"GitHub","optional":true}],"status":"live","first_seen_at":"2026-09-09T20:05:24Z","employer_posted_date":"2026-09-26","last_verified_at":"2026-10-29T01:58:36Z","board_verified":true,"closed_at":null,"days_open":49,"trust":{"level":"ok","repost_count":null,"flags":[],"days_open":49},"description":"About the role\nGATK, 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.\nThe 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.\nThe 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).\nWhat you'll do\nThe exact mix will flex with community and Institute needs, but the role generally spans:\nStandards & development\nAdvance 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.\nAuthor 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.\nRelease engineering & maintenance\nDrive a regular release cadence across the repositories, ensuring updates reach downstream channels.\nTriage issues and review pull requests, working down a substantial backlog and prioritizing high-impact internal and community needs.\nCommunity, governance & communication\nHelp establish and run a Trusted Developer Program - recruiting and onboarding external contributors, administering a tiered access model, and maintaining governance documentation.\nSupport the user community, including monitoring and responding on the GATK forums.\nRepresent the project at conferences and community meetings (e.g. GA4GH) and help align priorities across collaborators and Broad programs.\nTooling & acceleration\nApply state-of-the-art AI/ML coding tools to accelerate review and development across large, complex, multi-language codebases.\nOver time, explore LLM-based tooling to help answer recurring community questions from existing documentation.\nEarly focus areas\nSequencing and timelines will be set with the hiring manager, but early work is likely to center on:\nAdvancing priority standards work such as VCF 4.4.\nStanding up the Trusted Developer Program and re-establishing a regular release cadence.\nActively updating the source repositories to modern AI-friendly standards.\nWhat we're looking for\nExcellent written and verbal communication and a collaborative, community-facing disposition. \nSubstantial professional software engineering experience building and maintaining production-grade systems.\nTypically 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.\nProficiency in Java/JVM languages or a demonstrated track record of becoming rapidly productive in a large, mature, multi-language codebase.\nStrong Python skills for tooling, analysis, and pipeline work.\nExperience writing, testing, and deploying bioinformatics workflows in WDL or NextFlow.\nDeep working knowledge of genomics/bioinformatics: sequencing data and core file formats (BAM/CRAM/VCF/BCF), variant representation, and large-callset processing.\nDemonstrated ownership of open-source or shared infrastructure, code review, release management, and sustaining quality in a codebase many others depend on.\nExperience designing or operating large-scale cloud data pipelines (GCP, AWS, or Azure).\nComfort adopting AI-assisted development workflows.\nInterest in learning new technologies and programming languages, such as Rust. \nStrongly preferred\nPrior hands-on experience with the GATK ecosystem (GATK / HTSJDK / Picard) or other Broad genomics infrastructure (GenomicsDB, Terra, GCS-based workflows). \nFamiliarity with genomic file-format internals and compression (e.g., htslib, noodles).\nMLOps background and ML/AI pipeline tooling experience.\nExperience in regulated/GxP clinical or production environments.\nEngagement with GA4GH or other genomics standards bodies. \nTech environment\nJava/JVM\nPython\nGitHub-based open-source workflow\nDocker\nGCP\nGA4GH file-format standards\nAI-assisted development tooling\nThe 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.\nAt 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.\nThe 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.\nShould you need a reasonable accommodation to complete the application or interview process, please contact  for assistance.","description_format":"text","description_chars":6105,"description_truncated":false,"requirements":{"experience_years_min":10,"management_years_min":null,"team_size_min":null,"manages_managers":false,"education":{"level":"bachelor","optional":false},"security_clearance":false,"languages":[]},"benefits":["Retirement plans"],"hiring_locations":[],"hiring_excludes":[],"relocation_offered":false,"industries":["Bioinformatics","Genomics & Genetic Testing","Nonprofits & Foundations","Research Institutes"],"lifecycle":[{"event":"open","at":"2026-09-09T20:05:24Z"}],"visa":[],"liveness":{"score":15,"band":"cold","label":"Long shot","p_open":1,"p_active":0.426,"p_room":0.35,"age_days":48,"expected_fill_days":12,"reasons":["conf:2","velocity","win:tail"],"computed_at":"2026-10-28T05:59:10Z"},"pay":null,"html_url":"https://alion.io/job/broad-institute-principal-software-engineer-gatk","json_url":"https://alion.io/job/broad-institute-principal-software-engineer-gatk.json","meta":{"generated_at":"2026-10-29T04:44:09Z","cache_seconds":300,"methodology":"https://alion.io/methodology","terms":"https://alion.io/terms","contact":"https://alion.io/contact","api":"https://alion.io/developers","about":"Alion is a live layer of people, companies and AI agents: who they are, whether they are real and active right now, what they do and how to work with them, readable by people and by agents and paid per call.","catalog":"https://alion.io/catalog.json","usage":{"tier":"crawler_verified","counted_by":"address","units_charged":1,"used_today":7327,"day_limit":null,"remaining_today":null,"minute_limit":300,"resets_at":"2026-10-30T00:00:00Z"}},"offers":[{"id":"company.slices","title":"One company in depth, by slice","status":"live","price":{"credits":0.02,"usd":0.002,"plus_per_slice":{"credits":0.05,"usd":0.005}},"unit":"per company, plus each slice with data","note":"the employer in depth","call":{"mcp_tool":"get_company","arguments":{"id":15717},"rest":"https://alion.io/mcp/rest/get_company?id=15717"},"human":"https://alion.io/catalog?offer=company.slices&for=job%2Fbroad-institute-principal-software-engineer-gatk"},{"id":"market.stats","title":"A market slice: pay, demand and time to fill","status":"live","price":{"credits":1,"usd":0.1},"unit":"per slice","note":"pay, demand and time to fill for this role and place","call":{"mcp_tool":"market_stats"},"human":"https://alion.io/catalog?offer=market.stats&for=job%2Fbroad-institute-principal-software-engineer-gatk"},{"id":"job.search","title":"Open jobs by role, technology, place, pay and visa","status":"live","price":{"credits":0.02,"usd":0.002},"unit":"per posting in a list","note":"similar open postings","call":{"mcp_tool":"search_jobs"},"human":"https://alion.io/catalog?offer=job.search&for=job%2Fbroad-institute-principal-software-engineer-gatk"},{"id":"company.verify","title":"Is this company real and active right now","status":"pilot","price":null,"unit":"per company","request":{"url":"https://alion.io/catalog/request","method":"POST","body":"{\"offer\": \"company.verify\", \"for\": \"job/broad-institute-principal-software-engineer-gatk\", \"note\": \"what you need it for\"}"},"human":"https://alion.io/catalog?offer=company.verify&for=job%2Fbroad-institute-principal-software-engineer-gatk"}],"agent":{"mcp":"https://alion.io/mcp/jobs","mcp_open":"https://alion.io/mcp/open","next":[{"tool":"get_job","arguments":{"id":578845}},{"tool":"search_jobs","arguments":{"company":"broadinstitute.org","detail":"compact"}},{"tool":"match_people","arguments":{"job_id":578845},"note":"people open to offers who fit this vacancy"}],"note":"The same data through MCP tools: https://alion.io/mcp/open needs no sign-in (compact searches, postings, people); https://alion.io/mcp with an Alion account has everything. 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