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.
This position will involve collaborating with teammates to develop software and pipelines to expand the types of variants detectable with our clinical sequencing pipelines as well as tools for tertiary analysis of variants, including clinical classification. This position requires a high-performing bioinformatics programmer with demonstrated exceptional communication, organization, and time-management skills to assist in building and operating these pipelines.
Position is located at our main Baylor Campus in the Texas Medical Center.
Clinical Production Informatics
- Benchmark new bioinformatics tools for inclusion in production pipelines.
- Implement pipeline steps in AWS batch and lambda or local HPC system.
- Develop and deploy docker containers for pipeline components.
- Support and troubleshooting pipelines.
- Interact with Project Managers, Clinical Geneticists, LIMS, and IT.
- Provide feedback to NGSI Production R&D.
- Build and maintain monitoring tools.
- Maintain documentation of software to CAP/CLIA standards.
- Bachelor's degree in Genetics, Biology, Bioinformatics, Biostatistics, Computational Biology, Computer Science, or a related field.
- Four years of relevant experience.
- Master’s degree in a related field may be considered in lieu of two years of required experience.
- Experience in the following:
- Unix command line interface
- Programming Language (python preferred; ruby, java, perl, C++)
- Familiarity with databases and sql.
- At least 1 year of at-scale NGS experience.
- Experience working on large software engineering, projects, strong understanding of change management processes.
- AWS / Cloud services including cloudformation, batch, lambda, SNS, ECR, DynamoDB
- CAP/CLIA Documentation
- High Performance Compute Environment (e.g., moab, PBS)
- Software testing
- NGS sequence analysis tools (e.g., BWA, Samtools, bedtools, Dragen)
Baylor College of Medicine is an Equal Opportunity/Affirmative Action/Equal Access Employer.