Biomedical Informatics Data Specialist

• 3+ years of Python and Bash scripting
• Writing Snakemake or similar pipelines
• HPC computing
• Contribute code with team members using git
• Bioinformatics
• Human Clinical Genomics
• OMIM, Gnomad, ClinVar, HGMD, and other databases
• Handling and exploring VCF files
• High level communication, documentation, organizational, and time-management skills

• Work closely with a small diverse team of scientists and engineers to deliver high-quality data
• Document and design data models
• Extract, integrate, and reconcile new data sources with existing knowledge bases
• Perform quality control on data to ensure that it meets requirements
• Working with the project team and an enterprise infrastructure team to test the impact of new functionality on data
• Experiment with new data management technologies and systems and prototyping solution
• Working within the developer team to share knowledge, collaboratively developing best practices
• Working with Stakeholders, Users, and Project Managers to meet NIH Project Goals and Milestones

• BS. or higher degree in computational life sciences or related field.
• Demonstrated expert fluency (3+ years working experience) in using Python for bioinformatics or biomedical informatics data management pipelines
• Experience with snakemake pipelines
• Proficiency in the use of UNIX/Linux and bash scripting
• Experience with high performance computing and cloud environments
• Experience with common clinical genomic file formats (primarily VCF, but also BAM)
• Experience using Git and GitHub for tracking code changes and sharing contributions of multiple team members
• Demonstrated experience extending the functionality of existing software; ability to learn an existing body of code and extend it.
• Experience with annotating human genomes with annotations through scripting and the use of reference genome databases
• Knowledge of public genomic databases such as OMIM, Gnomad, ClinVar, HGMD, others
• Excellent communication skills and ability to work with users, including to develop and document requirements
• Excellent organizational and time-management skills
• Experience communicating with end users on software development projects

Secondary Qualifications:

• Experience mapping reads to human genome reference databases and understanding of challenges in migrating annotations between genome reference versions (GRCH.37 / GRCH.38)
• Experience reviewing mapped reads using genome browsers such as IGV
• Experience working with human genome variant calling pipelines such as GATK
• Solid understanding of human genome annotation databases (gnomAD, 1000 genome, ExAC)
• Demonstrated knowledge of scientific data sources, data structures, and mapping data to models
• Demonstrated skills in extracting, integrating, and reconciling new data sources with existing knowledge bases

Bonus Qualifications:

• Experience with CLIA compliant clinical genomics pipelines
• Experience with the product LabKey
• Experience with developing data visualizations and dashboards
• Familiarity with relational and non-relational database systems (SQL, MongoDB, Neo4j)