Genomics Research Data Analyst — HPC Pipelines

University of California - San Diego Medical Centers; San Diego (CA); On-site; USD 90,000 - 120,000; Full time

Job summary

University of California - San Diego Medical Centers seeks a bioinformatics specialist to build and optimize computational pipelines for sequencing and genotyping in HPC and cloud environments. You will document workflows, ensure data quality, and contribute to data reporting across research projects.

The role requires strong scripting in Bash, Linux expertise, and experience with tools like PLINK, GATK, HipSTR and BEAGLE, plus programming in Python and R.

Qualifications

• Six years of related experience, education/training, OR a Bachelor's degree in related area plus two years of related experience/training.
• Working knowledge of research function.
• Working skills in statistical analysis, systems programming, database design and data security measures.
• Working skills in analysis and consultation.
• Skills to communicate complex information clearly in writing and speech.
• Knowledge of bioinformatics software related to sequencing and genotyping, with staying current in the field.
• Experience planning and conducting studies related to genotyping and genotyping QC, optimizing pipeline parameters.
• Knowledge of Linux-based workflow development, including Bash scripting.
• Experience developing multistep analysis pipelines/workflows using scripting languages including WDL.
• Experience handling big data sets; programming in R and Python.
• Knowledge of Linux, HPC, cloud technologies such as Amazon EC2, and the All of Us Research Workbench.
• Ability to manage time and complete assigned parts on deadline.
• Excellent communication skills.
• Working knowledge of sequencing and genotyping software such as Bcftools, Bedtools, FastQC, Plink, Vcftools.
• Documentation and code annotation proficiency; experience with Git.
• Experience performing genome-wide analysis of tandem repeats in human populations.

Responsibilities

• Build computational pipelines to perform sequence analysis and genotyping in HPC and cloud compute environments.
• Develop new pipelines under supervision, selecting software and testing different computational approaches.
• Document work and annotate code; organize and backup data.
• Handle research data reporting tasks of moderate diversity in scope and provide results under supervision.

Skills

Bash scripting

Linux

Bioinformatics pipelines

Genotyping analysis

GATK

PLINK

HIPSTR

BEAGLE

Python

R

Data security

Big data handling

Education

Bachelor's degree in related area

Tools

GIT

HPC

Cloud computing platforms

Amazon EC2

Job description

University of California - San Diego Medical Centers seeks a bioinformatics specialist to build and optimize computational pipelines for sequencing and genotyping in HPC and cloud environments. You will document workflows, ensure data quality, and contribute to data reporting across research projects.

The role requires strong scripting in Bash, Linux expertise, and experience with tools like PLINK, GATK, HipSTR and BEAGLE, plus programming in Python and R.