Title:  Programmer/Analyst II

Division:  Human Genome Sequencing Center
Schedule:  Monday - Friday, 8 am - 5 pm
Work Location:  Baylor Main Campus, Houston, TX
Salary Range:  $68,725 - $69,000
FLSA Status:  Exempt
Requisition ID:  3733
Job Purpose

The Human Genome Sequencing Center (HGSC) at Baylor College of Medicine was founded in 1996 under the leadership of Dr. Richard Gibbs and is a world leader in genomics. The the primary mission of the HGSC is actionable translational research across the full spectrum of human health and disease using large-scale genomic data to drive collaborative analytics, gene-phenotype discovery and clinical innovation. As a Center for Common Disease Genomics funded by the National Institutes of Health, the HGSC provides a unique opportunity to work on the cutting-edge of genomic science at the center of Houston's Texas Medical Center. With approximately 200 employees and occupying 36,000 square feet of Baylor's Alkek Building, the HGSC boasts state-of-the-art sequencing and High Performance Computing technology. Resources include a cluster with more than 3 million CPU hours per month sitting atop 8 PB of live disk, which serves as the foundation for high-throughput production, research analytics, software development, an expansive integration with AWS cloud-computing resources, and a local Hadoop distributed compute infrastructure. Over the next five years the HGSC will sequence more than 100,000 samples and manage close to 100 PB of data for both our research efforts and our newly established clinical lab, the HGSC-Clinical Laboratory.


The HGSC provides a unique opportunity to gain high-throughput data production experience in an academic research environment, with opportunities for publication, conference travel and international scientific collaboration. As a member of the NGSI Clinical Informatics team, you will directly contribute to the HGSC's pioneering work in Mendelian genomics and multiple NIH Precision Medicine initiatives. The next-generation sequencing informatics (NGSI) team oversees the day-to-day logistics of all NGS pipelines through the process of mapping, alignment, variant calling and quality control. Within that larger group, the HGSC-CL informatics team focuses on the center's growing list of clinical projects and partnerships. The many well-defined and funded HGSC projects offer our talented staff the freedom to innovate and the satisfaction of delivering actionable results.  Increasingly, these pipelines are moving towards a cloud infrastructure that is under development. This support-level position requires a high-performing programmer with demonstrated exceptional communication, organization, and time-management skills to assist in building and operating these pipelines. 

Job Duties

HGSC-CL Programmer / Analyst Duties: 

  • Clinical Production Informatics
  • Implement pipeline steps in AWS batch and lambda
  • Develop and deploy docker containers for pipeline components.
  • Support and troubleshooting this pipeline
  • Interact with Project Managers, Clinical Geneticists, LIMS, and IT
  • Provide feedback to NGSI Production R&D
  • Build and maintain monitoring tools
Minimum Qualifications
  • Bachelor’s degree in Computer Science, Management Information Systems, Information Technology, or a related field. Four years of related experience may substitute for degree requirement.
  • Two years of relevant experience. 
Preferred Qualifications


  • At least 1 year of at-scale NGS experience.
  • Unix command line interface
  • Programming Language (python preferred; ruby, java, perl, C++)
  • Familiarity with databases and sql.
  • Git


The ideal candidate will also have the experience with some of the following:

  • Software Engineering
  • AWS / Cloud services including cloudformation, batch, lambda, SNS, ECR, DynamoDB
  • CAP/CLIA Documentation
  • High Performance Compute Environment (e.g., moab)
  • Software testing





Baylor College of Medicine is an Equal Opportunity/Affirmative Action/Equal Access Employer.