Title:  Bioinformatics Programmer II

Division:  Human Genome Sequencing Center
Schedule:  Monday - Friday, 8 am - 5 pm
Work Location:  Baylor Main Campus, Houston, TX
Salary Range:  $50,251 - $70,000
FLSA Status:  Exempt
Requisition ID:  6267


The Human Genome Sequencing Center (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 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

Clinical Production Informatics

  • Implements pipeline steps in AWS batch and lambda or local HPC system.
  • Develops and deploys docker containers for pipeline components.
  • Supports and troubleshoots this pipeline.
  • Interacts with Project Managers, Clinical Geneticists, LIMS, and IT.
  • Provides feedback to NGSI Production R&D.
  • Builds and maintains monitoring tools.
  • Maintains documentation of software to CAP/CLIA standards.
  • Assists the larger NGSI team as necessary.

Minimum Qualifications

  • Bachelor's degree in Computer Science, Biological Science, or a related field. 
  • Two years of relevant experience.

Preferred Qualifications

  • Master’s degree in a related field may be considered in lieu of the required two years of experience.
  • At least 1 year of at-scale NGS experience
  • Experience in the following:
    • 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, 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.