Sr. Bioinformatics Programmer

Baylor College of Medicine
Job Location
Houston, TX
Job Description

The Next-Generation Sequencing Informatics (NGSI) group is looking to hire an individual who is seeking to continue a challenging and rewarding career as a Senior Bioinformatics Programmer. As the bioinformatics core of the HGSC, NGSI oversees the day-to-day logistics of all NGS pipelines through a single, integrated system that supports the HGSC Sequencing and Analysis Efforts. As a senior NGSI member, this role will contribute to the development, testing and deployment of new protocols and the transition of existing methods to production scale. These efforts will engage the full spectrum of HGSC projects, ranging from rare Mendelian disorders to large disease cohorts (Alzheimer's, Heart Disease, Cancer) to model organism integration. In this role, the Senior Programmer will work with internal and external collaborators to support the publication and communication of actionable scientific findings at conferences.

Operating at a scope rare even in industry, the HGSC provides a unique opportunity for qualified bioinformatics professionals to gain high-throughput, production-quality experience in an academic research environment, with opportunities for publication, conference travel and international scientific collaboration. The many well-defined and funded HGSC projects offer our talented staff the freedom to innovate and the satisfaction of delivering actionable results A qualified candidate will possess a minimum of two years of at-scale NGS experience and the ability to drive NGS pipeline development and contribute to HGSC software engineering. This senior-level position requires a high-performing programmer and scientist with demonstrated exceptional communication, organization, and time-management skills. This candidate will “hit the ground running” and so must be proficient in all and an expert in most of the skills listed in the “Experience” section listed below.

  • Pipeline Maintenance and Development: PM, LIMS, QC, IT, Clinical feature requests.
  • Novel Protocol Implementation.
  • Continuous Integration Testing.
  • Advanced Ticket Resolution.
  • Production Integration with Data Warehouse, DNAnexus.
  • HGSC Software Engineering.
  • Maintain and Develop NGSI software.
  • Integrate into production environment.
  • Parliament, Eris, CNV tools, Afterburners, Annotation




  • B.S in Bioinformatics, Computer Science
  • 3 years’ experience in scientific programming with applications to genome research or a Master’s degree in Computer Science or Biological Sciences and 1 year of directly related work experience.
  • Experience in the following:  Unix / Bash / Command Line Interface,  Programming Language (python preferred; ruby, java, perl, C++), NGS tools, Bamtools, Bedtools, Picard, GATK, NGS formats, BAM/SAM/CRAM, VCF, bed, fastq, High Performance Compute Environment (e.g., moab), Illumina Whole-Genome, Whole Exome, Capture NGS data, Software Development, github/sourceforge 



  • 2 years of at-scale NGSC experience.
  • LIMS, Hadoop, HiSeq X, NGS Variant Calling, At-Scale Production, Software Engineering
How to Apply


To apply:

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

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