Research Data Analyst II - Genomics & Cloud Pipelines

UC San Diego Health; San Diego (CA); On-site; USD 90,000 - 120,000; Full time

Job summary

UC San Diego Health (Department of Pediatrics) seeks a skilled professional to build and optimize computational pipelines for sequencing and genotyping. You will work in HPC and cloud environments, using Bash, PLINK, GATK, HipSTR, BEAGLE, and related tools to process large genomic data sets.

The role requires strong documentation, collaboration, and the ability to communicate complex analyses clearly. Experience with Linux, cloud computing, and genome-wide analyses is essential, with a focus on

Qualifications

• Six years of related experience, or a Bachelor's degree plus two years of related experience.
• 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 verbally.
• Knowledge of bioinformatics software related to sequencing and genotyping.
• Proven ability to plan and conduct genotyping studies and QC.
• Knowledge of Linux-based workflow development, including Bash scripting.
• Experience developing multistep analysis pipelines using scripting languages including WDL.
• Experience with big data and programming in R and Python.
• Knowledge of Linux, HPC, cloud technologies (AWS), and All of Us Workbench.
• Proven ability to manage time and complete tasks on deadline.
• Excellent communication skills.
• Familiarity with sequencing and genotyping software like bcftools, bedtools, FastQC, Plink, vcftools.
• Documentation and version control experience (e.g., GIT).
• Experience genome-wide analysis of tandem repeat variation in human populations.

Responsibilities

• Build computational pipelines for sequence analysis and genotyping in HPC and cloud environments.
• Perform routine quality control for data inputs and analysis outputs.
• Develop new pipelines and test different computational approaches under supervision.
• Carefully document work and annotate code, ensuring reproducibility.
• Collaborate with team members and help meet project deadlines.

Skills

Bioinformatics

Genotyping

Linux scripting

GIT

Cloud computing

HPC

Data analysis

R

Python

Education

Bachelor's degree in related area

Tools

PLINK

GATK

HipSTR

BEAGLE

Bcftools

Bedtools

FastQC

R

Job description

UC San Diego Health (Department of Pediatrics) seeks a skilled professional to build and optimize computational pipelines for sequencing and genotyping. You will work in HPC and cloud environments, using Bash, PLINK, GATK, HipSTR, BEAGLE, and related tools to process large genomic data sets.

The role requires strong documentation, collaboration, and the ability to communicate complex analyses clearly. Experience with Linux, cloud computing, and genome-wide analyses is essential, with a focus on